Wow, that really IS whack.
I know of nothing that can delete a partition like that except a virus or partitioning program. Something is probably going wrong either hardware wise or with your master partition table on the HDD.
I don't think it would be a magnetic problem - hard drive magnetic fields are very very weak - putting two HDDs on top of one another does not affect them at all, either when running or not. The strength of magnetic fields drops off expodentially with distance and the fields present in a HDD operate only at very very very close ranges (fractions of millimeters). Modern HDDs in fact have several platters inside each with a separate magnetic head that can read and write to it. The magnetic fields operating on the heads are so weak they only affect the platter they're meant to, and never adjacent platters. Magnetic influence (from within the HDD) can therefore be ruled out.
You've ruled out the motherboard as a possibility by getting a new one, and you've tested the RAM (not that this should be the problem from the symptoms). The IDE cables shouldn't be the problem if the problem comes and goes - and if you've reinstalled windows on the cables, they are more than likely fine. Still - your motherboard most likely came with new cables - be sure to use them and not the old ones, just to eliminate another (very minor) possibility.
If it was the HDD that was going completely and not just losing partitioning information I'd suspect your power supply (the Hard Drive not receiving enough power to spin up and report its partition information), but if it's reporting that there IS a HDD there but that its unpartitioned, this doesn't seem like the answer either. Data is stored on the HDDs magnetically - so even if it didn't receive power for a while, and then did, the data will still be there when it powers up.
*censored*. You've eliminated most of the likely causes and there is no obvious candidate left. Pull out everything you dont need (all those PCI cards etc) and see what happens. This should leave your motherboard, memory, processor, one HDD a keyboard, mouse, power supply and video card. Given you've replaced the mobo and HDD if you're still having problems this would leave the memory, processor, k/b, mouse and video card as potential sources of difficulty. I'd then be tempted to test these in other machines to eliminate them. Can't think of what else to do.
