Hi DEV,
looks like you've found a bug. Even with the fix for the issue I mentioned in 0.8.0, there's still a bug when you have two nested subprocesses. This has to do with the way the filename for the subprocess is calculated.
You'll have to fix this yourself if you're sticking with 0.6.0, so here's how:
Open up the org.activiti.designer.eclipse.util.Util.getSubProcessURI(Diagram, String). The method body should be this instead of what's in there now:
final URI baseURI = diagram.eResource().getURI().trimFileExtension();
final String calculatedExtension = subprocessId.replaceAll("_", ".");
final URI subProcessURI = baseURI.appendFileExtension(calculatedExtension).appendFileExtension(diagram.eResource().getURI().fileExtension());
return subProcessURI;
Debug that method when saving your main process and it should pass back a valid URI for BOTH subprocesses.