Check for a virus, some virii slowly changes your filenames until it corrupts your whole hard drive. Some programs for data recovery are: FinalData.Enterprise, GetDataBack, Runtimes.Diskexplorer, SpinRite. It does sound like something hosed your filesystem. A program I use to check SMART status, as well as voltages and fan speeds is Speedfan (
www.almico.com/speedfan.php). If your SMART status is OK, then your hard drive is physically OK, so a reformat would fix everything (besides you losing all your data).
I recommend using NTFS, it is newer, has more security features, does not get fragmented as easily as FAT32, and it's apparently more stable.