Hi Dave,
Sounds like a things you might want to check out...
First off, programs running fine and then suddenly starting to go slow, means either a virus or overheating... Running something like Supreme Commander would have a great affect on your graphics cards, so suggestion would be to pop out both your graphics cards and run one of them at a time, making sure they are seated properly... Test SC on one card, adjusting the settings to max, and see how it goes... If it runs fine for double or either tripple the time with the single card in, do the same with the other card...
**EDIT** Just read an interesting note regard a chap who had simular problems it seems, ends up he forgot to plug the dedicated power into the cards...
If both test out fine on their own, seat both cards in the machine, making sure of the connections and also the SLI bridge being seated properly... Before testing the heck out of it, pop on over to the
nVidia Drivers Page for the card, and get the newest drivers. The page linked goes to the correct driver for Windows XP...
Update the drivers, go into the settings after the reboot and if it has a testing page, run the tests and make sure SLI is working... Reboot the machine again for a clean start and go see what happens with SC...
I know ATi with their Radeon products have a self-overclock component which actually stresses the GPU's and gets the max out of them, all the while showing what the temperatures are on the cores... You might want to have a look at that... If either one of the cards fail while testing, it might be the card that's gone, if they only fail when in SLi, might I suggest a fan directly above the two cards in order to get their temps down... Generally though, when a graphics card fails, it is either because of drivers or because of a failure of the chip itself instead of heat, GPU's are made to run hot...
Next point would be to do a general sweep of all the components on your motherboard, and making sure it is seated properly... pop everything out, (cpu not needed i reckon), and reseat it so that you are 100% sure they are properly seated...
I suspect it might be a seating problem, so give that a go and we will take it further from there... Many sites suggest that this might in fact be a power problem, but I've never seen hassles on the Thermaltake PSU's, so not to keen on that being the issue. If all else fails, and you have a spare PSU lying around or can borrow one from a friend, give it a go...
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Point of interest... XP Pro v 9.00.2.000 is a scary thought, I'm running version 5.1.2600, and that is XP Pro Service Pack 2, newest Service Packs and all... if you click your start button, click run, type in "cmd" and press enter... When the window comes up, type in "ver" and press enter... Will show you the version you are running...
If all else fails, get back to me and we will take it from there...
All the best!
Riaan
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