I'm not sure if I stumbled upon a major bug, a 3.71 firmware problem, or just bad luck but Picodrive committed suicide on me last night. The emulator completely deleted itself and all of the files and folders in its own directory except the bin file, which was everything including the save files!!!
It has actually happened twice. The first time wasn't so bad because I was just testing games, so I didn't really notice it but this time I lost over a week of saves because it has been the only thing I have been playing.
It may be related to Lunar 1 I think it happened both times after I loaded the iso and then loaded a save state at the sega logo. After that saves failed. When I checked the memory stick, everything in the picodrive folder was gone!
I tried to force it to happen again but it didn't work. Now I've downgraded to 3.52 in hopes that it won't happen again because this emulator just rocks
Fornatting my card seems to have fixed the slowdown issue I was having, and I haven't had any other problems since then, so maybe it was just my card's fault. Keeping my fingers crossed...