With my Ati 9500 Non Pro the results of harware rotation were half mixed with Mame.
It was more likely the specific card and Catalyst driver but my bottom 1/3 of the screen was clipped and I fiddled and fiddled to no end.
I was using a custom vertical layout also to display mamewah and that part worked out fine it was just launching games the clipping was there. I gave up and started playing with Gamelauncher since it is built in to rotate the orientation and I didnt have to resort to any harware our software settings.
Im sure there are alot of ATi cards that wont have this problem but in my case I have a sapphire oem version and it might not be up to par.