R4-Spirit Tracks erased "cant find DS MENU.DAT" ?!?

So i've been using my R4 (old broken spring version) and using the original firmware with YSMenu sometimes and sometimes not depending on what games and cheats I need to access. I can run recent games just fine (RC Soccer Hooligans)on it so I haven't switched over to the Wood fw yet.

Anywho, I loaded up Zelda: Spirit Tracks for the first time under YSMenu. It asked to create a save bookmark like usual, so I clicked OK...loaded for a bit, and then popped up "save file corrupted..etc". I couldn't do much else so I turned off the DS and turned it back on. The R4 goes to load and I instantly get a black screen with "R4 can't find DS_MENU.DAT" and that's it. I took the SD card and popped it in my PC and EVERYTHING on it is gone.....WTF?!? I looked up and heard that Tracks can mess up your save once you're in the game but have it completely wipe my SD card? I mean there is NOTHING left on there according to my PC. No games/saves/folders/text docs....nothing. Showing Just under 2 GB free space on a 2GB card.
I haven't seen anyone else have this problem. I guess this wasn't a patched Tracks, and instead the clean one.
I haven't tried formatting because i'm hoping it's a mistake. I didn't know the R4 could format an SD card on it's own. Is it possible my R4 is damaged/broken? Are there other games that have been known to do this??