Just out of curiosity, when you paused your game, did you leave it on the Menu or Options screen and minimize it? If so, your games weren't really paused, due to the way that the game handles game speed changes. The safest thing to do when you're not going to be actively playing the game and want it to be paused for some period of time is to pause it and then quit. Your game will be saved in a paused state and will be preserved, ready for you to resume at a later time.

If the game is running and minimized, it is susceptible to problems resulting from computer crashes, etc.