Simon Kingaby got a working setup with autopatch talking to MS-SQL using ant.
He documented his configuration in the hopes it would help future folks.

Here's his configuration:

Project Structure:
------------------

trunk
-->HelloWorldDatabase
  (build.xml)
---->src
------>main
-------->conf
        (log4j.properties)
        (migration.properties)
-------->db
---------->patch
          (patch0001_create_table.sql)
-->vendor
---->build
------>sqljdbc_1.1
-------->enu
        (sqljdbc.jar and other sqljdbc files and folders)
------>tk-autopatch
      (tk-autopatch-1.0.2.jar and other autopatch files and folders)


Here is the migration.properties file:
--------------------------------------
orchestration.context=zabbadoo
orchestration.controlled.systems=zabbadoo
zabbadoo.jdbc.database.type=sqlserver
zabbadoo.jdbc.driver=com.microsoft.sqlserver.jdbc.SQLServerDriver
zabbadoo.jdbc.url=jdbc:sqlserver://kobol\\dev;database=zabbadoo
zabbadoo.jdbc.username=zabbadoo
zabbadoo.jdbc.password=password
zabbadoo.patch.path=db.patch


Here is the ant build.xml:
--------------------------
<?xml version="1.0" encoding="UTF-8"?>
<project name="zabbadoo" default="patch.info" basedir=".">

   <property name="autopatch.dir" value="../vendor/build/tk-autopatch" />
   <fileset id="autopatch.jars" dir="${autopatch.dir}">
       <include name="tk-autopatch-*.jar" />
       <include name="lib/*.jar" />
   </fileset>

   <property name="msjdbc.dir" value="../vendor/build/sqljdbc_1.1/enu" />
   <fileset id="msjdbc.jars" dir="${msjdbc.dir}">
       <include name="**/*.jar" />
   </fileset>

   <fileset id="dependent.jars" dir="${basedir}">
       <include name="**/*.jar" />
   </fileset>

   <path id="patch.classpath">
       <fileset refid="autopatch.jars" />
       <fileset refid="msjdbc.jars" />
       <fileset refid="dependent.jars" />
       <pathelement location="${basedir}/src/main/" />
       <pathelement location="${basedir}/src/main/conf" />
   </path>

   <target name="patch.info" description="Prints out information about
patch levels">
       <java   fork="true"
               classpathref="patch.classpath"
               failonerror="true"
               logError="true"
               classname="com.tacitknowledge.util.migration.jdbc.MigrationInformation">
               <sysproperty key="migration.systemname"
value="${ant.project.name}"/>
       </java>
   </target>
   <target name="patch.database" description="Brings up the databases
to the current patch levels">
       <java   fork="true"
               classpathref="patch.classpath"
               failonerror="true"
               logError="true"
               classname="com.tacitknowledge.util.migration.jdbc.StandaloneMigrationLauncher">
               <sysproperty key="migration.systemname"
value="${ant.project.name}"/>
       </java>
   </target>
</project>