Hardware problem - Harddrives randomly disappearing

A couple weeks ago I started having a problem with the harddrives in my system randomly "disappearing." At first, it was just my secondary harddrive (which has my personal files on it) - it wouldn't be there when I tried to save something to it, then randomly it would show up again (Windows would give me the "hardware was just connected!" message). Shortly after I started noticing this, my boot drive also started disappearing on startup.

I can duplicate this problem by starting the system, letting it run a while, then trying to reboot. The system doesn't recognize a bootable drive, and checking the BIOS shows me a blank space (rather than text that says nothing is connected, like it's supposed to be) where my drive should be.

My initial thought was that my power supply was either dead or not supplying enough power, but all the voltages are right, and a watt meter tells me I'm pulling less than 250W when the system is under moderate stress. (I'm running a 520W PSU) Because of the randomness of the problem, I assume the problem is either the motherboard itself, or a simple problem of overheating. However, I don't have a spare motherboard to test everything, and I'm skeptical about it being overheating because it doesn't need to be running very long for the problem to show up. (I did run some tests on both harddrives to be safe, as well as the memory, and they all passed just fine)

Before I go out and spend a couple hundred dollars on components so I can test my system, I'd like some advice on what else I can try first to pinpoint the issue. What else might be causing this problem? And how can I test it to be certain?

My hardware is as follows:
Gigabyte EP45-DS3R Motherboard
Intel Core 2 Duo E8400
8 GB RAM (4x 2GB)
2x GeForce 9600GT
Corsair 80+ 520W PSU