The same thing is happening to me. I have trashed Flash preferences repeatedly (actually, ~/Library/Preferences/Macromedia/Flash Player) and that used to work. Yesterday, I used System Preferences>Flash Player>Storage, clicked Delete All and then Delete All Site Data and Settings. I reset my preferences and, so far, they seem to be sticking. Apparently, Delete All also clears ~/Library/Caches/Adobe/Flash Player so that may have been the cure.
