Windows 7 - Second GPU repeatedly disappears!

I am baffled with this one. I'm running two GTX 465's in SLI on a Gigabyte Z68XP-UD4 motherboard. I have a Corsair 850 watt PSU, with 70A on the 12v rail. Windows 7 Home Premium 64 bit. For whatever reason, my second GPU keeps disappearing from Device Manager altogether. When I go to Nvidia Control Panel, there is no longer a set SLI option, it only shows "Set PhysX configuration." To troubleshoot the cause of this problem, I uninstalled all drivers, ran Driver Sweeper, and installed the latest Nvidia drivers for each GPU separately. Then, I put them both in and got SLI working. I then rebooted my computer. After the reboot, I created a System Restore point, with SLI still fully working. After this, I would go about playing games and what not. I literally do not change a thing on my system, but I'll randomly reboot and there's no second GPU. No SLI anymore. I go to System Restore, and restore it to the point where I had fully working SLI, and it reboots to the same problem. No SLI, no second GPU detected. I am so frustrated with this.

There are a number of things that could have happened here. Firstly, is it possible that one of the cards may not be seated correctly? Remove and reseat both cards, blowing the slots out to remove any dust that might be causing poor connections. Don't forget the SLI bridge connector and the auxiliary PSU connectors. Secondly, one of the cards might have gone bad. Try running with just one card and then swapping it for the other one. Another possibility is insufficient power from the PSU (unlikely, given its rating). To check this, back-probe the auxiliary power connectors with a digital multimeter. You should get a reading of 12V ±5% between any pairings of yellow and black wires.

Well, I was about to do all this, then the SLI config started to work again. When I was troubleshooting I decided to enable onboard VGA in my BIOS, just to see what would happen. I rebooted and now I have SLI again. I'm so baffled. Since then, I've done a complete shutdown and reboot and it is still working just fine. Thanks for the help Dwarf, if it goes out again I will follow your advice.

Okay, so I just booted up my computer again. SLI not available. No second GPU in the device manager. I did not do ANYTHING. It just disappears!