jBPM goofs with the created XML. Have a look at the referenced schema or open it in something like XMLSpy, that will tell you what's wrong. Its usually just an incorrect order of elements. Do not edit the xml outside of Eclipse. For some unknown reason - I haven't had time or interest to find out :-( - the editor looses it when the xml is edited externally.
The schema is being worked upon at this very time. Look for the upcoming release or have a peek in CVS. The issue with GPD losing it is a bit more complicated. I'll have to work on a decent import and node layout algorithm to solve that.