Have you checked your SD Card, or if your HDD is multi-partitioned, made sure that the FAT32 portions of the filesystem aren't damaged?
Download this package, run it on your SD card, since I've found out that my program might not run in a wbfs file system... Not too sure.
..report the contents of the folders here. =)
BTW, have you updated/modified the contents of anything other than games within that year of perfect operation?