We'll need more information. That bug has been reported once or twice before and IIRC it was caused by mods. Try save/quit while not using any mods at all and see if it still happens.
Confirming that disabling all the mods seemed to have fixed the issue. I'll try enabling them one by one and see which one triggers that behavior. Seems mine does, in fact. Here is the mod itself, anyone know what might be wrong with it? I hope this is just my toy version and not the one I published recently. ... Okay I figured out why this was happening. When you run a mod out of a folder, Dredmor does not, apparently, simply ignore parts of that folder that isn't, in fact, part of the mod, and if you add enough junk to that folder eventually dredmor decides to stop saving your games. So best to develop the mod somewhere else and drop the zip file in your mods folder.