First, I installed VanillaMod 0.93 and the emergency fix on M2TW v1.3. Today, I edited in musketeers for England. To do this, I had to unpack all the data packs using the unpacker, because I didn't have them before when I first installed VanillaMod. Launching the game now through the VanillaMod.bat, my saves are gone, according to the game. I can look in the saves file, however, and they're still there.
What's going on? Can I force the game to read those saves somehow, or place them where they will be read?