I saw a similar issue when I upgraded to windows 7 a couple of years ago. on the initial install screen res was just fine but after a few updates I couldn't get the VGA input on my monitor to set the correct resolotion (1680X1050). It has to do with the way windows reads the resolution information form the display. VGA (analog) uses a different method from HDMI (digital). Only thing I could figure was that Win7 was updated to use the digital mode and somehow the analog mode got broken. It was very annoying.
You video card should have at least one or two DVI outputs. Try getting a DVI to HDMI cable. I have two identical monitors and one is connected with a DVI to DVI cable and the other is connected with a HDMI to DVI cable. Since both DVI and HDMI are digital it works just fine.