Shadowgate was the NES game I noticed it immediately with… The music is all distorted and choppy…Mario is fine, till you get going quickly and there are several enemies… SNES games are worse… It almost undos the mid level over-clock…
Bumping the sleep up higher helps, Shadowgate is not as choppy, but it is noticeable enough still that you can hear in the music when it recycles… What I have not tried yet is seeing if I increase the sleep and if bumping the over-clock a little more will help…
I posted on the raspberry pi forums as well and it was suggested there that I look into finding a script that does the same but uses polling or interrupts and it not BASH based… So I am going to explore that as well…