Yep, if you mainstream the CAB, you need to stay on vertical.
I did have the same problem in Arcade Music Box in ealier versions, but I got it fixed, before I lost the source. I remember it crashed to.
It pretty normal the desktop is rotated as well for mainstream issues. Otherwice it hard to see, what you doing in windows.
So authors of AtomicFE and GameEX (as I saw on a other thread): I hope this bug got fixed, so it can been used regaardless window desktop is rotated or not.
You can also look on MALA wich as was intended for use with vertical monitor. But mamewah is also a great frontend, when it configurated correct.
NB. Sorry about this offtypic.