Originally Posted by gildedlink
Considering how late this post is to the thread, maybe I shouldn't bother asking for more info -_-
Does it run so fast under windows as well?
There are a few normal things you may have done within the program, for example there is a speed key that you may have mapped as a button as well (an easy mistake to make), options such as frame skip, Real Time Clock, and more may have something to do with it.
The most likely conflict I can see with Linux may be how the emu has an option to set the process priority...