When I use the below mapping I get null results back from the getParents() method if parents is mapped with inverse="true", while the getChildren() method returns accurate results.

If I change so that children is mapped as inverse="true" I get the opposite. getParents() return accurate results and getChildren() returns null values. See last row in log for an example of getParents(). Reading the log seems to return 2 objects, but the method call lists 6 result where 5 are null.

Running the same query inside of MySQL returns correct result.

Hibernate version:
3.1.3

Mapping documents:
<class name="MyObject" dynamic-update="true" dynamic-insert="true" table="objects" abstract="true" lazy="false">
<id name="id" type="long" unsaved-value="null" column="id">
<generator class="native"/>
</id>
<version name="version" unsaved-value="null" column="version"/>
<property name="guid" type="string" column="guid"/>
<property name="name" type="string" column="name"/>
<property name="type" type="string" column="type"/>
<list name="parents" table="object_links" cascade="none" inverse="true">
<key column="child_id" not-null="true"/>
<list-index>
<column name="sort_order" not-null="true"/>
</list-index>
<many-to-many column="parent_id" entity-name="com.elanders.cn.cms.model.CmsObject"/>
</list>
<list name="children" table="object_links" cascade="all">
<key column="parent_id" not-null="true"/>
<list-index>
<column name="sort_order" not-null="true"/>
</list-index>
<many-to-many column="child_id" entity-name="com.elanders.cn.cms.model.CmsObject"/>
</list>
</class>
...
joined subclasses removed
...

Code between sessionFactory.openSession() and session.close():
object.getChildren();
object.getParents();

Name and version of the database you are using:
MySQL 5.0.19

The generated SQL (show_sql=true):
Debug level Hibernate log excerpt:
Hibernate: select parents0_.child_id as child1_1_, parents0_.parent_id as parent2_1_, parents0_.sort_order as sort3_1_, cmsobject1_.id as id2_0_, cmsobject1_.version as version2_0_, cmsobject1_.guid as guid2_0_, cmsobject1_.name as name2_0_, cmsobject1_.type as type2_0_, cmsobject1_1_.name as name4_0_, cmsobject1_2_.name as name5_0_, cmsobject1_2_.short_name as short3_5_0_, cmsobject1_2_.password as password5_0_, cmsobject1_2_.network as network5_0_, cmsobject1_2_.home as home5_0_, cmsobject1_2_.email as email5_0_, cmsobject1_3_.name as name6_0_, cmsobject1_4_.name as name7_0_, cmsobject1_4_.short_name as short3_7_0_, cmsobject1_4_.password as password7_0_, cmsobject1_4_.network as network7_0_, cmsobject1_4_.home as home7_0_, cmsobject1_4_.email as email7_0_, cmsobject1_5_.name as name8_0_, cmsobject1_5_.url as url8_0_, cmsobject1_6_.name as name9_0_, cmsobject1_6_.bit_value as bit3_9_0_, cmsobject1_7_.name as name10_0_, cmsobject1_7_.permission_value as permission3_10_0_, cmsobject1_8_.name as name11_0_, cmsobject1_8_.assigned_type as assigned3_11_0_, cmsobject1_8_.default_name as default4_11_0_, cmsobject1_8_.constructor_class as construc5_11_0_, cmsobject1_8_.show_in_tree as show6_11_0_, cmsobject1_8_.is_inline_object as is7_11_0_, cmsobject1_8_.can_nest_self as can8_11_0_, cmsobject1_8_.auto_create as auto9_11_0_, cmsobject1_8_.display_scope as display10_11_0_, cmsobject1_8_.display_mode as display11_11_0_, cmsobject1_8_.display_page as display12_11_0_, cmsobject1_8_.edit_page as edit13_11_0_, case when cmsobject1_3_.object_id is not null then 3 when cmsobject1_4_.object_id is not null then 4 when cmsobject1_1_.object_id is not null then 1 when cmsobject1_2_.object_id is not null then 2 when cmsobject1_5_.object_id is not null then 5 when cmsobject1_6_.object_id is not null then 6 when cmsobject1_7_.object_id is not null then 7 when cmsobject1_8_.object_id is not null then 8 when cmsobject1_.id is not null then 0 end as clazz_0_ from object_links parents0_ left outer join objects cmsobject1_ on parents0_.parent_id=cmsobject1_.id left outer join structures cmsobject1_1_ on cmsobject1_.id=cmsobject1_1_.object_id left outer join actors cmsobject1_2_ on cmsobject1_.id=cmsobject1_2_.object_id left outer join groups cmsobject1_3_ on cmsobject1_.id=cmsobject1_3_.object_id left outer join users cmsobject1_4_ on cmsobject1_.id=cmsobject1_4_.object_id left outer join modules cmsobject1_5_ on cmsobject1_.id=cmsobject1_5_.object_id left outer join permissions cmsobject1_6_ on cmsobject1_.id=cmsobject1_6_.object_id left outer join roles cmsobject1_7_ on cmsobject1_.id=cmsobject1_7_.object_id left outer join prototypes cmsobject1_8_ on cmsobject1_.id=cmsobject1_8_.object_id where parents0_.child_id=?
2006-06-13 23:57:58,375 DEBUG org.hibernate.jdbc.AbstractBatcher - preparing statement
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.LongType - binding '32' to parameter: 1
2006-06-13 23:57:58,375 DEBUG org.hibernate.jdbc.AbstractBatcher - about to open ResultSet (open ResultSets: 0, globally: 0)
2006-06-13 23:57:58,375 DEBUG org.hibernate.loader.Loader - result set contains (possibly empty) collection: [com.elanders.cn.cms.model.CmsObject.parents#32]
2006-06-13 23:57:58,375 DEBUG org.hibernate.engine.CollectionLoadContext - uninitialized collection: initializing
2006-06-13 23:57:58,375 DEBUG org.hibernate.loader.Loader - processing result set
2006-06-13 23:57:58,375 DEBUG org.hibernate.loader.Loader - result set row: 0
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.LongType - returning '26' as column: id2_0_
2006-06-13 23:57:58,375 DEBUG org.hibernate.loader.Loader - result row: EntityKey[com.elanders.cn.cms.model.CmsObject#26]
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.IntegerType - returning '1' as column: clazz_0_
2006-06-13 23:57:58,375 DEBUG org.hibernate.loader.Loader - Initializing object from ResultSet: [com.elanders.cn.cms.model.Structure#26]
2006-06-13 23:57:58,375 DEBUG org.hibernate.persister.entity.AbstractEntityPersister - Hydrating entity: [com.elanders.cn.cms.model.Structure#26]
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.IntegerType - returning '0' as column: version2_0_
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.StringType - returning '3DA0A241-CF38-BCE4-278D-BD07D617B344' as column: guid2_0_
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.StringType - returning 'Permissions' as column: name2_0_
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.StringType - returning 'Permissions' as column: type2_0_
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.StringType - returning 'Permissions' as column: name4_0_
2006-06-13 23:57:58,375 DEBUG org.hibernate.engine.TwoPhaseLoad - Version: 0
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.LongType - returning '32' as column: child1_1_
2006-06-13 23:57:58,375 DEBUG org.hibernate.loader.Loader - found row of collection: [com.elanders.cn.cms.model.CmsObject.parents#32]
2006-06-13 23:57:58,375 DEBUG org.hibernate.engine.CollectionLoadContext - reading row
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.LongType - returning '26' as column: parent2_1_
2006-06-13 23:57:58,375 DEBUG org.hibernate.event.def.DefaultLoadEventListener - loading entity: [com.elanders.cn.cms.model.CmsObject#26]
2006-06-13 23:57:58,375 DEBUG org.hibernate.event.def.DefaultLoadEventListener - attempting to resolve: [com.elanders.cn.cms.model.CmsObject#26]
2006-06-13 23:57:58,375 DEBUG org.hibernate.event.def.DefaultLoadEventListener - resolved object in session cache: [com.elanders.cn.cms.model.CmsObject#26]
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.IntegerType - returning '5' as column: sort3_1_
2006-06-13 23:57:58,375 DEBUG org.hibernate.loader.Loader - result set row: 1
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.LongType - returning '35' as column: id2_0_
2006-06-13 23:57:58,375 DEBUG org.hibernate.loader.Loader - result row: EntityKey[com.elanders.cn.cms.model.CmsObject#35]
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.IntegerType - returning '1' as column: clazz_0_
2006-06-13 23:57:58,375 DEBUG org.hibernate.loader.Loader - Initializing object from ResultSet: [com.elanders.cn.cms.model.Structure#35]
2006-06-13 23:57:58,375 DEBUG org.hibernate.persister.entity.AbstractEntityPersister - Hydrating entity: [com.elanders.cn.cms.model.Structure#35]
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.IntegerType - returning '0' as column: version2_0_
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.StringType - returning 'F5D621FC-944A-C73A-4C66-762AD5A28B59' as column: guid2_0_
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.StringType - returning 'Role Permissions' as column: name2_0_
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.StringType - returning 'RolePermissions' as column: type2_0_
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.StringType - returning 'Role Permissions' as column: name4_0_
2006-06-13 23:57:58,375 DEBUG org.hibernate.engine.TwoPhaseLoad - Version: 0
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.LongType - returning '32' as column: child1_1_
2006-06-13 23:57:58,375 DEBUG org.hibernate.loader.Loader - found row of collection: [com.elanders.cn.cms.model.CmsObject.parents#32]
2006-06-13 23:57:58,375 DEBUG org.hibernate.engine.CollectionLoadContext - reading row
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.LongType - returning '35' as column: parent2_1_
2006-06-13 23:57:58,375 DEBUG org.hibernate.event.def.DefaultLoadEventListener - loading entity: [com.elanders.cn.cms.model.CmsObject#35]
2006-06-13 23:57:58,375 DEBUG org.hibernate.event.def.DefaultLoadEventListener - attempting to resolve: [com.elanders.cn.cms.model.CmsObject#35]
2006-06-13 23:57:58,375 DEBUG org.hibernate.event.def.DefaultLoadEventListener - resolved object in session cache: [com.elanders.cn.cms.model.CmsObject#35]
2006-06-13 23:57:58,375 DEBUG org.hibernate.type.IntegerType - returning '5' as column: sort3_1_
2006-06-13 23:57:58,453 DEBUG org.hibernate.loader.Loader - done processing result set (2 rows)
2006-06-13 23:57:58,453 DEBUG org.hibernate.jdbc.AbstractBatcher - about to close ResultSet (open ResultSets: 1, globally: 1)
2006-06-13 23:57:58,453 DEBUG org.hibernate.jdbc.AbstractBatcher - about to close PreparedStatement (open PreparedStatements: 1, globally: 1)
2006-06-13 23:57:58,453 DEBUG org.hibernate.jdbc.AbstractBatcher - closing statement
2006-06-13 23:57:58,453 DEBUG org.hibernate.loader.Loader - total objects hydrated: 2
2006-06-13 23:57:58,453 DEBUG org.hibernate.engine.TwoPhaseLoad - resolving associations for [com.elanders.cn.cms.model.Structure#26]
2006-06-13 23:57:58,453 DEBUG org.hibernate.engine.CollectionLoadContext - creating collection wrapper:[com.elanders.cn.cms.model.CmsObject.parents#26]
2006-06-13 23:57:58,453 DEBUG org.hibernate.engine.CollectionLoadContext - creating collection wrapper:[com.elanders.cn.cms.model.CmsObject.children#26]
2006-06-13 23:57:58,453 DEBUG org.hibernate.engine.CollectionLoadContext - creating collection wrapper:[com.elanders.cn.cms.model.CmsObject.nodes#26]
2006-06-13 23:57:58,453 DEBUG org.hibernate.engine.TwoPhaseLoad - done materializing entity [com.elanders.cn.cms.model.Structure#26]
2006-06-13 23:57:58,453 DEBUG org.hibernate.engine.TwoPhaseLoad - resolving associations for [com.elanders.cn.cms.model.Structure#35]
2006-06-13 23:57:58,453 DEBUG org.hibernate.engine.CollectionLoadContext - creating collection wrapper:[com.elanders.cn.cms.model.CmsObject.parents#35]
2006-06-13 23:57:58,453 DEBUG org.hibernate.engine.CollectionLoadContext - creating collection wrapper:[com.elanders.cn.cms.model.CmsObject.children#35]
2006-06-13 23:57:58,453 DEBUG org.hibernate.engine.CollectionLoadContext - creating collection wrapper:[com.elanders.cn.cms.model.CmsObject.nodes#35]
2006-06-13 23:57:58,453 DEBUG org.hibernate.engine.TwoPhaseLoad - done materializing entity [com.elanders.cn.cms.model.Structure#35]
2006-06-13 23:57:58,453 DEBUG org.hibernate.engine.CollectionLoadContext - 1 collections were found in result set for role: com.elanders.cn.cms.model.CmsObject.parents
2006-06-13 23:57:58,453 DEBUG org.hibernate.engine.CollectionLoadContext - collection fully initialized: [com.elanders.cn.cms.model.CmsObject.parents#32]
2006-06-13 23:57:58,453 DEBUG org.hibernate.engine.CollectionLoadContext - 1 collections initialized for role: com.elanders.cn.cms.model.CmsObject.parents
2006-06-13 23:57:58,453 DEBUG org.hibernate.engine.StatefulPersistenceContext - initializing non-lazy collections
2006-06-13 23:57:58,453 DEBUG org.hibernate.loader.Loader - done loading collection
2006-06-13 23:57:58,453 DEBUG org.hibernate.event.def.DefaultInitializeCollectionEventListener - collection initialized
2006-06-13 23:57:58,453 DEBUG com.elanders.cn.cms.service.impl.CmsManagerImpl - OBJECT PARENTS: [null, null, null, null, null, Role Permissions (35)]