I have one OS, but Computer Management says I have system files on 2 hard drives. If I remove the drive with system files on it that doesn't have my OS on it, windows fails to boot.
I think that If I unplug the hard drive that says it has system files on it, but no other files (ex programs, the OS, ect.), then reboot and put in a recovery disc and tell it to fix any start up problems, that it might resolve my issue.
Then after that I'll put the empty unplugged drive in my external bay, boot my laptop with gparted and format the drive in the external bay so the whole 500mb of system files is gone. Then after I get my desktop to boot without the other drive that had system files on it, ill simply put the drive that was in the external bay back in.
Wish me luck.