Thanks for going to the trouble to provide so many details. I would prefer to leave possible solutions up to someone else. But just wanted to comment that your video card was originally put onto the market 10 years ago. Not that this should be an issue however. I'm not a Windows fixer (Mac) which is why I'd prefer someone else to help you. I also have the 8800 card except mine is the 750 MB Vram version (gtx I think) after my first two died (previous gts a year ago.)

Have you perhaps tried reducing the monitor resolution? Have you tried changing the interfacing setting on the monitor(s) between DVI and Analogue?
Are you using an interface converter between the monitors and computer (such as DVI to HDMI, etc.)?
You said you tried running the main monitor from both ports right? Just to be sure both still work.