Usually when you get files out of a source control system, they will be marked as read only. So if you are editing a Java file in Eclipse, you will get a dialog box coming up asking you to make the file writable. Now consider what happens with jBPM:

Most likely you will check in the gpd.xml file. Otherwise, other people trying to view your processdefinition.xml file will not get a very viewable image. (Everything will appear in the top left.)

When you start editing your processdefinition.xml file, the picture you see will be updated. Everything will appear to be fine. However, none of the changes are saved to the gpd.xml file. When you shutdown Eclipse and restart, the gpd.xml will be out of step with the processdefinition.xml.

I think this could be fixed fairly easily with a couple of lines of code that check the writable status of the gpd.xml file and change it if necessary. Obviously the workaround is just to manually change the write flag, but it is a bit of a "gotcha" and can lead to work being lost if you don't know to do that.