This seems really weird. I've doublechecked everything but this issue does not happen to me at all, although I've might heard about it once.
Viewing post in Old Bug Report Thread
I just did a reinstall and went straight into a random game, encounters work fine. I think the problem came when I tried to change and save the Constants. It's the only thing that was different, and the only time this has bugged out on me was this version. The Constants would save and be usable in a game until I exited the game, next time I boot up the game, the Constants reset. So I think that should be the problem.