There are several crashes between levels that I recall but I believe the most prominent cause on Linux to be related to music playback. JJ2 uses parallel threads incorrectly and, as far as I could tell, assumes that one will finish its work in time for the other to have it available. Multiple Linux users reported that disabling music in the game options reduces or completely eliminates crashes; although this was said about JJ2+ before this fix rather than about vanilla JJ2.
Because the error is related to how multithreading was designed in that part of code, a proper fix would be fairly complicated. The fix I wrote for it is essentially an equivalent of duct tape; it doesn't look great, or work great, but at least the hole is gone until a better solution is in place. I can try to help you adapt it to vanilla JJ2 but first please provide the address your crash occurs at to confirm that's it.
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I am an official JJ2+ programmer and this has been an official JJ2+ statement.
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