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Blimey! I'd be very fed up aswell if I splashed out all that money on *that* card only to have worse FPS! Something is definitely wrong.
How much worse is it compared to the 8800GTX?
What power supply do you have?
Did you uninstall the 8800 gts drivers before putting in and booting up with your new 280 GTX?
How are other games performing? Did you ever run 3Dmark on your old 8800 GTS if so run them and compare them to 280 GTX.
Something other than the graphic card is the performance bottleneck in the configuration. Probably a hardware setup thing less likely in view of recent OS-reinstall a 3rd party software issue.
Take a look at these testers. Maybe one of them can help you.
http://www.rightmark.org/