I have the same issue trying to run three displays, two vertical on each side and one horizontal in the center.
I have two graphics cards (NVIDIA GeForce 8800 GT and NVIDIA GT 120).
I can rotate with those plugged into the GT 120, but not in the 8800 GT. Tried changing the order of plugging in and everything, and every other tip I could find online, but still couldn't get 90 or 270 degrees to work on the displays plugged into the 8800 GT.
I'm only seeing the "black screen" and a mouse pointer. I can drag and blindly click content on those black screens, just can't see it.
Seems it must be some simple issue to reproduce and correct.
My system is a MacPro3,1 3 GHz Quad-Core Intel Xeon. The 8800GT is the stock card that came with the machine. The GT 120 is a about 2 years old and was added to power a newer Apple LED Cinema Display (black trim), the other two monitors are the older Apple Cinema Displays with the silver trim.
I first noticed the issue when i upgraded from Mac OS 10.7 Snow Leopard to Mac OSX 10.8 Mountain Lion and from there the monitor / display rotation didn't work - again just a black screen and a mouse pointer on the rotated display.
At this point I've got one rotated vertical and two horizontal as that's the best I could do.
Any suggestions for a fix would be appreciated.