Wow, that is crazy, and not something I've ever seen. I take it that doing any of the Add Loop commands from the session menu just does nothing in this case? If you then remove them all, when you add them back does it always stop at the same number?
As a workaround since it seems to work with loaded sessions, is to hand edit the session file, which is in very readable XML format. You can totally specify how many loops and what their settings are, just base it on the ones you make.
I wish I could reproduce this!