Sounds to me like there are two possibilities here.
#1: You have a faulty SATA controller
#2: You have a faulty SATA cable
If two drives both exhibit the same symptoms and at least one of those drives appears to work fine in a different system, then that points the finger pretty clearly at there being something wrong with your system.
Here are my computer specs:
Apevia 680w - power supply
Nvidia 8800GTS 320mb - video card
Seagate 250gb 7200 rpm SATA - Primary Harddrive
Seagate 320gb 7200 rpm SATA - Secondary Harddrive
EVGA Nvidia nforce 680i - Motherboard
Intel Core 2 Duo 2.66 ghz - Processor
Now to my problem. When I first built my computer the only harddrive I had was the 250gb. A little while after I bought another 250gb SATA for extra storage space but everytime I started up my computer the secondary harddrive would disconnect after a half hour. So then I sold the harddrive (the harddrive works fine with the new owner) and about a week ago bought a new harddrive thinking that it could have just been the other harddrive not wanting to work with my computer. But the same thing is happening. It isn't exactly a half hour everytime. Sometimes it can take 15 minutes before it disconnects. I have checked temps inside my computer but nothing is remotely high. Anyone know what is going on?