Hi Eric,
Could you please explain why you think you need the <jarModule> definitions for the ComConfiguration and ComCommon jars ? They are regular jars and do not contain EJB's right? Assuming this is true, then they are not expected to show up in the deployment.xml as this one only shows real modules in the JEE sense.
You say that you do see them in the looseconfig.xmi and that's good. In your original post, you said that things worked as long as you keep these two projects closed and that it does not work when you open them. What happens in the looseconfig.xmi in these two cases?
Finally, we've had an issue with websphere in the 'run from workspace' mode, regarding jars that are present both in the WEB-INF/lib of a war module and in the lib/ directory of the ear. In this case the classes were not accessible and threw ClassNotFoundExceptions. I don't have the access to the PMR number, but it was a won't fix error, so we are just very careful to avoid this situation now.
Regards, Marcel