MadShots,
I am no pro--this is just a suggestion, since I see no one else has tried to help. I had a similar thing happening before, and I traced it to my privacy settings. In Internet Options, General tab, there is a box for "Delete browsing history on exit." When I unchecked this box, my Flash settings were no longer affected.
That was a while ago. Now, I think that the Flash settings are supposed to be kept separate from the Explorer browser settings; but it wouldn't hurt to try this if you are still experiencing the problem.
Brett