Things to try:
1. Check your bios setup and see if both your sata drives are being properly detected;
2. Get the hard drive manufacturer's diagnostic utilities from the manufacturer's website; all the majors have them. They are available in the form of a bootable iso that that you burn to a cd-r and run the diagnostics off the cd from boot. Run the thorough version on each or your hard drives and see if any errors are reported;
3. Get a linux livecd like knoppix, sidux, slax, etc. Boot with the livecd and see if it can properly see both hard drives and all partitions on those hard drives. You can check how linux sees your drives by running as root from a terminal: fdisk -l. Note any errors;
4. Download the current version of memtest(I think it might be on the sidux live cd) and run memtest for several hours to thoroughly test your ram.
What you describe sounds like a hardware problem, bad hard drive or corrupted mbr, bad ram or possibly a bad power supply. The above steps will help you diagnose the cause of your problem and limit things down a bit. Yours sounds more hard drive related, possibly some corruption of the mbr/partition table.
If all else fails and the above diagnostic steps don't uncover anything unusual, you can back up your /home from fedora to some external media and zero fill both drives using the manufacturer's diagnostic utilities. This will completely wipe all data from both drives so be sure to backup first. A zero fill will write zeros to every sector of the hard drive and leave the hard drive in the same condition as when it left the factory. Sometimes when mbrs get really messed up, particularly when you use both windows and linux partitioning utilities like you have, a zero fill is the only way to get things working again.
Last edited by kilgoretrout; 05-14-2008 at 02:44 PM.