There is an advanced settings option in JK1 (it's activated by running the game with a command line IIRC), I just don't know what it is. Advanced options setting... try searching for that. It's from a long time ago.. but somebody figured it out. Like a debug mode!
JK1 has always run fine for me, but maybe there's something in there that can help you.
Also look up "JK Auto Save converter" (autosave converter or something similar) for if your game crashes and you lose something (back up your save files too just in case!)