After some more investigation, it appears at least some, and potentially all of this problem is a merely visual bug. So when you toggle a breakpoint inside a run fsm template, it will show all these wrong scrambled values inside the template as outlined in previous posts. But in all the cases I've tested thus far, the output is still correct as long as the code inside the template is good.
Even if it a purely visual error, this is still a huge problem though IMO. It makes debugging templates inside a runfsm basically impossible as many of the variables you see at your breakpoint are wrong. You can paste the template into a test fsm and set it up there, but that's a pretty large hassle for what should be a simple debugging process. I'll do some more testing to see if my runFSMs functionality actually breaks when set up correctly.