I'm running 1.04e and Firmware 4 with a 32GB Sandisk Extreme Card formated to FAT32 with 32kb cluster size as advised. I ran a cheap 8GB SD card before and had the same thing happen, that's why I upgraded. My problem happens very randomly, sometimes when resetting via the hardware button sometimes when playing different games. So far I lost a Pokémon yellow save and various others GB and GBC as well. This happened on OG GB, GBC and GBP. Files are not long filenames, in folders plus checked...
EZFlash Jr. Loosing Saves
EZFlash Jr. Loosing Saves