Schema Correctness Check
In our use of XJC we have seen a similar problem (see the link below) that was solved by disabling the schema correctness check:
Try the following System property to disable the schema correctness check.
-Dcom.sun.tools.xjc.api.impl.s2j.SchemaCompilerImpl.noCorrectnessCheck=true
For Ant, try:
<xjc target="src">
<schema dir="src" includes="**/*.xsd" excludes="**/debug.xsd"/>
<arg value="-nv" />
</xjc>
From the following page the -nv parameter relates to the schema correctness check:
Getting into the Code
You could try interacting with XJC programmatically (see below) and plug-in your own EntityResolver to see where the import/include fails:
import com.sun.codemodel.*;
import com.sun.tools.xjc.*;
import com.sun.tools.xjc.api.*;
SchemaCompiler sc = XJC.createSchemaCompiler();
sc.setEntityResolver(new YourEntityResolver());
sc.setErrorListener(new YourErrorListener());
sc.parseSchema(SYSTEM_ID, element);
S2JJAXBModel model = sc.bind();