I'm having the same problem, too.
I'm currently running 4 monitors, both on nvidia hardware, with two on an older FX 5500, and the other two on my newer 9400 GT. It took some doing to make the different generations of drivers play nicely together.
I think that Windows is having a problem combining the images from framebuffers in different physical RAM locations (half on one card, half on the other).
That's my guess anyway.
The symptoms are the same: alt-printscreen works like a champ, but the whole-desktop printscreen seems like it doesn't even capture a picture. Photoshop usually is aware of the size of the image in the clipboard, and ctrl-n will create a new document with those dimensions. The size of my desktop is 5120x1024, but the new document is created at 900x1585 (probably just the size of whatever I last pasted in there).
I should have plenty of RAM. I tried reducing the hardware acceleration on all four monitors to the minimum level, and still nothing happens. I turned off write combining, and that might do something (just a stab in the dark though), but I won't know till after I reboot.
For now, Gadwin Printscreen (free download) did the trick, but it only captured my primary screen.