Ok, read the whole thread and I see that the OP isn't exactly new to these things and has tried just about everything. So, if it's not anything obvious, it must be something else: have you checked you have the latest mobo bios? And if possible, see if there's any update for you graphics card bios. A long shot I know and hard to see how it could affect this, but it might be worth a try
Also, give us that screenie of process explorer like one of the other members asked previously. There might be something locking/capping to the monitor refresh, you never know.
@The Mac
I see where you're coming from with vsync, but I've also seen fractional frame rates with vsync on, such as 45, 55 and other weird values, so there's probably something going on with the rendering engine to make it look like this. I used Fraps for the readout and I was using an HD 4870 at the time.
It's ironic that my current system is too high performance to try this out, lol. I'd have to downgrade it with one of my old graphics cards.