Those are definitely some weird problems. I guess here is an obvious question: Did you patch JA to the latest version? If so the only thing I can think of is to uninstall JA, reinstall it, update it, reinstall the demo and try again.
I had issues like this to begin with too. My suggestion is to remove all third-party pk3s (ie. all the stuff that didn't come with the game originally) from your Base folder to somewhere else (anywhere that JA won't find them).
Then you'll have a clean copy of JA running and the MOD should work fine.