Hi Don,
I don't have a fix, but I can confirm this behaviour. At least, to a point. I can't say for sure if running the agent while "dirty" subsequently prevents future saves, as you observed, but I will pay closer attention now to see if that is what is happening.
Incidentally, I have the property set to save the design element when the Java code is saved. This works very often, but then I get the situation you describe in which the agent itself does not save, even though the individual Java source code editors will save. However, if you cannot finally save the agent, those changes are lost.
It's frustrating.