Slow Sata II 0 port on GA-X48-DQ6

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I have a gigabyte GA-X48-DQ6 with 4g of ram and a Quad core extreem. Its been up and running for a few months now with no problems. Last week it sarted booting slow and it would hang during use. I have windows XP. I thought c drive (10k Velociraptor) was failing. I tested the drive on another machine and it checked out great. I found out my SATAII0 port was running very, very slow. I plugged it in to the SATAII1 port and my computer sprung back to life. Anyway I have no idea what would cause this. I have gone through the BIOS several times. It seems to have started a short time after I installed Virtual PC with vista on the same drive. It all works fine on the other sata port though.
 
I was posting because I thought there might be something else causing the problem. I was also wondering if I may have caused the failure by using Virtual PC on the same drive as the operating system?
I will flash the BIOS and see if that fixes it.
 
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