Hello, all! I am new to this forum, so be nice! Just kidding. While I am not new to the computer world, I do not know everything! 
I have a custom build PC, with an Intel DG31PR mother board. I will list the specs below;
Motherboard: DG31PR v1.0 with latest BIOS from Intel download center PRG3110H.86A.0071.2010.0318.1704, 3/18/2010
CPU: Intel Core 2 Duo e8400 @ 3.0 GHz Wolfdale LGA 755 Socket
Graphics: ATI Radeon HD3400 Series
RAM: 2GB DDR2
Hard Drive Config:
(I know they are laptop drives, it doesn't seem to matter. The issue persists on 3.5" hard drives).
-SATA 0: Hitachi 250 GB 2.5" HDD
-SATA 1: Western Digital Scorpio Black 500GB 2.5" HDD
-SATA 2: Western Digital Scorpio Black 500GB 2.5" HDD
Optical Drive Config:
-IDE 0: Optaric CD/DVD-RW Drive
-IDE 1: Random CD Drive
OS: Windows 7 Home Premium
There are no further modifications to the system, and no other installations. Here is the problem;
My system is severely slow when I have more than one SATA hard disk connected to the board. As soon as I remove the multiple drive(s), it is no longer an issue. This has been going on since I built the system back in 2010. I have tried different hard drives, different configurations, different drivers, operating systems, removed hardware including graphics card, USB ports, and optical drives, etc. The hardware configuration does not matter whatsoever outside of the physical drives, more than one SATA hard drive causes the system to constantly have the drive activity light on, and becomes frequently unresponsive and longer POST times. I have tried replacing cables, and even re-flashed the BIOS just in case there was an error. No BIOS changes to the SATA configuration makes no changes. I am starting to assume that the motherboard's SATA controller is defective.
P.S. The southbridge chip runs quite warm (79°C, 173°F). I have seen this as an issue with other owners of the DG31PR, as other users have complained about it here on the forums. I have added a heat sink to no avail to cool down the chip, it runs too hot to touch it physically. I believe these two issues to be related (maybe an internal short?) but it could just be normal. I have also ran a Memtest on my RAM, it checked out okay.
All opinions offered, and I am prepared to accept that I may need to purchase another motherboard with the LGA 755 processor socket. Thanks in advance everyone!