Try (enabling and) logging into the Guest account, and see if the problem happens there. If it doesn't happen there, then it has to do with the Flash settings or preferences or Flash-style cookies or cached files in your main account.
If you don't mind losing your Flash settings, and possibly having to re- log into some Flash-using sites, and possibly losing saved progress on some online Flash games and things like that, you could just delete the folders where Flash stores settings and cookies and caches.
This is one of the big ones:
rm -r ~/Library/Preferences/Macromedia
To find other paths worth investigating, run a command like this:
find ~/Library -iname '*macromedia*' -o -iname '*flash*' -o -iname '*adobe*'
Be judicious with what you choose to delete. Consider moving the current stuff aside, perhaps by dragging it to your Desktop, rather than simply deleting it.