I am experiencing the following problem.
<hibernate
destination="${build.gen-src.dir}"
package="${name}.hibernate"
genXDocletTags="false"
genIntergratedCompositeKeys="false"
/>
if you set

genXDocletTags="true"
genIntergratedCompositeKeys="true"

E get weblogic parse error.

I assume you mean that one (or more) of the class mappings are not parsing correctly for hibernate. Yes this could be the case even with the mapping being valid. There are two possibilities.
1) You are using hibernate 2.1 features and not using hibernate 2.1. This can occur in some of the one to one mappings and some other places. It is minor but there. or
2) The Xdoclet stuff required some changes to the DTD to validate correctly. Your options are;
a) Get the latest DTD from CVS and use it
b) Use Ant to generate the mappings twice, eg, first time round the mappings include XDoclet then hbm2java them. Once complete then generate without the XDoclet markup for persistence operations.
c) Upgrade to the lastest 2.1 beta of Hibernate.

If you have explored the above and still having problems then please isolate the mapping and include it and your environment and submit the details.

BTW: Why did you enable both options. You can choose to set one or the other depending on what you are after.