If it helps, I had to save and reload before I even exited the first area. Perhaps that caused an issue?
Also, out of curiosity, when am I supposed to learn new spells as a Mage? I think I got up to level 7, but I didn't learn any new spells, nor did I get any new weapons. Granted, my sapphire wand was already doing awesome enough, but still. This may be related to the Mage-thinks-he's-a-fighter glitch.
Cleric's pretty fun, though, what I could play before experiencing more crashing.
On that note, I did play around with the config file a bit after experiencing these problems. One of the things I did was add the skill "0" variable to it. Unfortunately, this hasn't fixed the problem of the difficulty resetting to "2" after closing and re-opening, but it might be a lead?