I've experienced that problem before, and it's one hell of a ***** to fix. It happens mostly with FF9. Epsxe can also use Bleem! and VGS memory card formats so I used my primary VGS mem card to save a game of FF9 that I was playing on epsxe. Then I tried loading the game in VGS and that's when it happened. It couldn't detect anything. I ejected the card and re-loaded and it said "This memory card has been corrupted beyond repair". I tried converting it multiple times but it didn't help. I had to make a new card, save a game on it with VGS, then use the epsxe memory card manager and copy the saved games back to the new card. Except that if you copy all the data directly it's still corrupted so you have to keep the game you saved on the new card still intact. Basically it was one hell of a mess. There's probably a better way to fix it but now I generally try to keep the two emulators seperate. I think it has to do with how FF9 is saved in epsxe. VGS requires a patch for FF9 and saves it differently.