Xpyburnt: How about making a players settings their default?
The game does so, ?in a cookie?
Thing is, CC Clean purges the cookies (or wherever storage is), so you command the loss of the settings.
OTOH, it may not be neccessary to use the program. I never did, and I also do not clear any caches (using FF), and the game runs fine here. It's enough to shut down all browser windows once or twice a day.
Meter ain't perfect but I fault that to Flash.