Stupid new computer issue.

This is just copied and pasted from one of the four boards I posted this issue to. Sorry if it reads funny.

I bought a new HP desktop about two weeks back. It came with a 640g hard drive but I needed my 500g from the old computer as well. Both are Western Digital SATA 3G 7200 rpm drives. The computer seems to run fine, until I start using the 500 drive. It will work fine for about 30 minutes, then everything will either come to a crawl, or just freeze. The only thing I have found to cure the freeze is to close explorer, and start it up again. After I do that, the drive (and most other things) is pretty much useless until I restart the computer. I’ve even tried to move everything from the 500 to the 640 while I try and trouble shoot, but even that is impossible.
And just a though, the 600 (the Windows installed drive) drive is plugged into SATA1 on the MB, DVD drive on SATA2, and 500 on SATA3. Any chance that makes a difference?

CPU: 2.2GHz AMD Phenom™ X4
RAM: 6GB PC2-6400 DDR2 SDRAM
Graphic: NVIDIA GeForce 9100
HDD: Western Digital 640GB SATA 3G 7200 rpm
HDD: Western Digital 500GB SATA 3G 7200 rpm
MB: Pegatron M2N78-LA
OS: Windows Vista Home Premium 64bit