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CHK DSK after new hardware installed

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Ok guys, here is a unique one... I have an HDDBoost with 120gig ssd, and 1TB HDD. I just got a new video card (switching from ati to nvidia). I also just got a new internal 1TB for media drive. Oh and I got a new wireless network card.

Here is what I did. Before removing my old AMD Card I uninstalled the drivers. I then installed all my hardware. I went to boot up and it hung on the BIOS. I've had issues with HDDBoost doing that in the past, so sometimes powering down, or unplugging the HDDBoost for 1 boot will fix the problem.

So I first unplugged the new 1TB drive. The boot still hung

Second, I unhooked HDDBoost, and new 1 TB Drive, and booted just off my system 1TB drive. It booted up fine. So since i had it booted up, in auto installed drivers for the network card. I then prceeded to install current drivers for the nvidia video card. I get this all done, and I did all this so that when I plugged the HDDBoost in it will just copy the new information over and I wouldn't have to worry about it.

I plugged HDDBoost back in and I recieved a CHKDSK on boot. I skipped past it, and found that everything was back to the way it was when I uninstalled the drivers. So I figured it booted off my HDDBoost SSD rather than the HDD. So I restarted the computer hoping it just didn't go through the copy phase it's supposed to. I boot again, it gives me the same CKDSK on boot. Once in Windows I try to install the Nvidia drivers again they wouldn't install, they fail on the first step. Also, the network card doesn't auto install like it did on the original HDD.

So I figure it a problem with the SSD and HDDBoost. I unplugged them and went back to my original set up with the System 1TB drive. I boot, and it now gave me a CHKDSK. I skip past, find that all the installation that I had done before also is not there, plus it won't let me install any driver again, and the network card is yet again not auto installed.

Currently I'm waiting on CHKDSK to finish going through my system 1TB drive.

I'm confused why this all happened. First, HDDBoost is not supposed to be able to change anything on my system drive, second why didn't it copy over, and third, why did my system drive even change in the first place?

Ok and last, How do I fix it without reinstalling windows and the 500 gigs of programs I have installed already?

Please help, trying to play BF3 Beta, sadly I got like 10 min of play with my old AMD card before I tried installing the hardware :)
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