Try this:
<exec executable="bash">
<arg line='-c "schemagen -d ../target/schema ../path/to/source/*.java"' />
</exec>
As we discussed above, the problem seems to be that on some Unix systems, the exec task does not expand wildcards. Thus this is an attempt to pass the command to a shell which will do the expansion for you.
And yes, I realize this solution makes the build.xml file unix-specific. If this works, there are ways to address that.