I had exactly the same frustrations with Windows 7 and Fraps (and Gadwin too, to be honest).
I got so annoyed that I sent a grumpy e-mail to their customer support, and they suggested loading Fraps after loading the game (so with the game running, Alt+TAB to your desktop, and start Fraps).
The good news is that this works for me every time, so perhaps it might solve your problem too?