My apologies for having forgotten about the test case. Here it is now. The zip contains a project. The project has a src dir with one groovy class. This class has a reference to a class from commons-math. The testscript uses the groovyc ant task, to compile the source class. No classpath elements have been assigned to the groovyc task.
If you execute the test script with groovy testscript.groovy, the compile fails, as it should be. There is no commons-math in the classpath.
If you execute the test script with groovy -cp lib/commons-math-1.1.jar testscript.groovy, the compile succeeds. This should not be the case, as we have set includeAntRuntime to false. If the isolation were working, you would need to assign the groovy and commons-math jar to the groovyc classpath to have a successful compile.
I had no time yet to give the above patch a try by myself.