I can run querys of the main table of the database just fine however Im running into some trouble trying to query associated tables, in this case specifically the associated strings element table called scholarshipXmajor.
Hibernate version:
hibernate-3.0.5
Mapping documents:
<?xml version="1.0" encoding="UTF-8"?>

<!--
Document : Scholarship.hbm.xml
Created on : March 1, 2005, 1:42 PM
Author : dsobiera
Description:
Purpose of the document follows.
-->

<!DOCTYPE hibernate-mapping
PUBLIC "-//Hibernate/Hibernate Mapping DTD 2.0//EN"
"http://hibernate.sourceforge.net/hibernate-mapping-2.0.dtd">

<hibernate-mapping>

<class name="edu.asu.SFAO.DAOs.Scholarship" table="scholarship">
<meta attribute="class-description">
A representation of an ASU scholarship
</meta>

<id name="id" column="scholarshipID" unsaved-value="0" >
<meta attribute="scope-set">protected</meta>
<generator class="native"> </generator>
</id>

<property name="name" type="string" not-null="true" column="name"> </property>
<property name="amountType" type="int" not-null="true" column="amount_type"> </property>
<property name="amount" type="int" not-null="true" column="amount"> </property>
<property name="activationDate" type="string" not-null="true" column="activation_date"> </property>
<property name="deadlineDate" type="string" not-null="true" column="deadline_date"> </property>
<property name="openDeadline" type="int" not-null="true" column="open_deadline"> </property>
<property name="applicationUrl" type="string" not-null="true" column="application_url"> </property>
<property name="needBased" type="int" not-null="true" column="need_based"> </property>
<property name="globalList" type="int" not-null="true" column="global_list"> </property>
<property name="minimumGpa" type="int" not-null="true" column="minimum_gpa"> </property>
<property name="minimumHours" type="int" not-null="true" column="minimum_hours"> </property>
<property name="azResident" type="int" not-null="true" column="az_resident"> </property>
<property name="condition" type="string" not-null="true" column="condition"> </property>
<property name="eligibility" type="string" not-null="true" column="eligibility"> </property>
<property name="description" type="string" not-null="true" column="description"> </property>
<property name="comment" type="string" not-null="true" column="comment"> </property>
<property name="contactName" type="string" not-null="true" column="contact_name"> </property>
<property name="contactOrganization" type="string" not-null="true" column="contact_organization"> </property>
<property name="contactPhone" type="string" not-null="true" column="contact_phone"> </property>

<set name="campuses" table="scholarshipXcampus" inverse="false" cascade="all">
<meta attribute="field-description">
A scholarship can have many campuses associated with it
</meta>
<key column="scholarshipID" />
<many-to-many class="edu.asu.SFAO.DAOs.Campus" column="campusID" />
</set>

<set name="classstandings" table="scholarshipXclassstanding" inverse="false" cascade="all">
<meta attribute="field-description">
A scholarship can have many classstandings associated with it
</meta>
<key column="scholarshipID" />
<many-to-many class="edu.asu.SFAO.DAOs.ClassStanding" column="classstandingID" />
</set>

<set name="donorPrefs" table="scholarshipXdonorpref" inverse="false" cascade="all">
<meta attribute="field-description">
A scholarship can have many donor preferences associated with it
</meta>
<key column="scholarshipID" />
<many-to-many class="edu.asu.SFAO.DAOs.DonorPref" column="donorprefID" />
</set>

<set name="majors" table="scholarshipXmajor" inverse="false" cascade="all">
<meta attribute="field-description">
A scholarship can have many majors associated with it
</meta>
<key column="scholarshipID"/>
<element column="majorCode" type="string"/>
</set>

</class>

<query name="edu.asu.SFAO.getAllScholarships" >
<![CDATA[
from edu.asu.SFAO.DAOs.Scholarship as scholarship
order by scholarship.deadlineDate ASC
]]>
</query>

<query name="edu.asu.SFAO.getGlobalScholarships">
<![CDATA[
from edu.asu.SFAO.DAOs.Scholarship as scholarship
where scholarship.globalList=1
order by scholarship.deadlineDate ASC
]]>
</query>

<query name="edu.asu.SFAO.getActiveScholarships">
<![CDATA[
from edu.asu.SFAO.DAOs.Scholarship as scholarship
where scholarship.activationDate <= :today and scholarship.deadlineDate >= :today
order by scholarship.deadlineDate ASC
]]>
</query>

<query name="edu.asu.SFAO.getSpecificScholarship">
<![CDATA[
from edu.asu.SFAO.DAOs.Scholarship as scholarship
where scholarship.id = :id
]]>
</query>

<query name="edu.asu.SFAO.getApplicableScholarships">
<![CDATA[
from edu.asu.SFAO.DAOs.Scholarship as scholarship
where scholarship.majors = :majors
]]>
</query>

</hibernate-mapping>

Code between sessionFactory.openSession() and session.close():
hibScholarshipSearchSession = sessionFactory1.openSession();
scholarships = hibScholarshipSearchSession.getNamedQuery("edu.asu.SFAO.getApplicableScholarships")
.setString("majors","-1")
.list();

Name and version of the database you are using:
ms sql (not sure verison)
The generated SQL (show_sql=true):
Debug level Hibernate log excerpt:

13:14:11,931 DEBUG SQL:324 - select scholarshi0_.scholarshipID as scholars1_, scholarshi0_.name as name3_, scholarshi0_.amount_type as amo
unt3_3_, scholarshi0_.amount as amount3_, scholarshi0_.activation_date as activation5_3_, scholarshi0_.deadline_date as deadline6_3_, scho
larshi0_.open_deadline as open7_3_, scholarshi0_.application_url as applicat8_3_, scholarshi0_.need_based as need9_3_, scholarshi0_.global
_list as global10_3_, scholarshi0_.minimum_gpa as minimum11_3_, scholarshi0_.minimum_hours as minimum12_3_, scholarshi0_.az_resident as az
13_3_, scholarshi0_.condition as condition3_, scholarshi0_.eligibility as eligibi15_3_, scholarshi0_.description as descrip16_3_, scholars
hi0_.comment as comment3_, scholarshi0_.contact_name as contact18_3_, scholarshi0_.contact_organization as contact19_3_, scholarshi0_.cont
act_phone as contact20_3_ from scholarship scholarshi0_, scholarshipXmajor majors1_ where scholarshi0_.scholarshipID=majors1_.scholarshipI
D and .=?
13:14:12,084 WARN JDBCExceptionReporter:71 - SQL Error: 170, SQLState: 37000
13:14:12,085 ERROR JDBCExceptionReporter:72 - Line 1: Incorrect syntax near '='.