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Hmmm... Do you do a lot of hard drive switching? Like do you often change your configuration, add, or remove drives? If so it might be a strange problem that I have run into where the bios actually seems to get confused and start putting in ghost drives. Drives that have been their before or not put anything in at all. I fixed that by reseting my bios. Before you do that though I'd look for another suggestion as most people have tweaked their bios up a bit.
What type of HD do you have? Also what is your mobo brand/model?
You say that apps freeze. That means you were actually in your OS? Then you rebooted, poked around and found your computer not to register them at all, and then rebooted it and it worked fine. Did it register any other drives i.e. cd-rom? If so that says HD. If not that says to look elsewhere.
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