That sounds like a driver interface issue to me. While writing this I found a nifty little tool called irotate. What it does is interface with the drivers of all the popular video cards and handles rotation itself. I had similar glitches before I started using it, but now everything seems to be working fine.
One of the cool things is it supports command line switching, so I'm currently re-writing part of my fe to work well with it. (Tell the fe not to rotate certain emulators while rotating others.... auto resizing of the skin when it's rotated, ect...)
I'll be using a wg hybrid monitor that is capable of svga resolutions (which I don't care for, but the price was right) so that stuff isn't as much of an issue for me. I'll also be usign a radeon 7000.
The pain about pivot pro is that it only rotates gdi applications, which means emulators and direct-x based front ends aren't effected. Works for mamewah though, luckily for you.

I'll probably run it at 1024x768, mainly because I plan on running some pc shooters which support vertical orientation and high resolutions.
I hope that helps some people.
Seriously, try out irotate, it rocks!