I have been working on this project/course for a long time and really, really enjoy the book. But I guess I should give up on the simulator projects.
Here is my original problem, and more to the point, this forum seems to have many examples of similar problems from other users, and none of them seem to have any real resolution.
I tried installing a newer JVM, different PC, disabling multi-core, etc. These have various effects but bottom line, the CPU Emulator in particular seems to be unusably unreliable.
I wish I had the energy to contribute to fixing this in the code, but that is not my expertise. Hopefully somebody will be able to at some point, it's such a fun idea/book. Sigh.