Something is borked up for sure.
Not to harp on ya after the fact, and my Conroe experience is nil at this point, but with all that new tech (Conroe processor, SLI board), I would have gone for a P5W (975X chipset) rather than the P5B (965). New CPU's on boards that "support" them but weren't designed for them from the ground up is always iffy. Especially when you then complicate it with a SLI-in-one video card.
It sounds like you're having a number of issues. The heat on the video card(s) suggests poor case ventilation. How many fans do you have running in that P180? Are you using that (terrible) fan shroud thingy on the side? If so take that off immediately. Do you have a 120mm fan at least on the back and top of the case?
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As for the wonky 3dmark results, it sounds like SLI is working and then stops working for the card -- as others have suggested, a fresh reformat and then clean install of the drivers would make the most sense for a card like that.
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Regarding your first card (X1900XT) - it does sound like it was defective - heating up to 100C after minutes, but sometimes issues like that can be fixed by simply reinstalling the heatsink and using better thermal paste (eg. Arctic Silver 5). Sometimes heatsinks can become loose in transit. Another option is buying aftermarket cooling - a ~$25 ish Accelero X1 (Nvidia) or X2 (ATI) works wonders!