While playing with several mods installed I've noticed something very annoying; occasionally when the game crashes the current Savegame and/or Autosave will be mysteriously deleted. and While I assume that the crashes themselves are most likely due to errors in the third party mods I have installed, those don't change how saved games are handled and so I can only conclude that there must be something fundamentally wrong with how the game handles saves.
Go to the documents/gaslamp games/dungeons of dredmor folder, you should see config.xml. Scroll down to the enableSteamCloud line and put that to 0 instead of 1