Probably not related but I had a somehow similar problem once. The PC mounted the card as a big floppy and the phone as a disk with partitions. Or vice versa, don't remember which. Anyway, for a while the effect was the PC seeing one set of files and the phone another. Inevitably, after a while, the FAT on the FAT partition was overwritten and bang! Card unreadable. I ended up writing a simple program to rescue my data. Didn't trust automatic tools to do that for me