In particular web sites, or whenever IE is opened?
I would try again. Uninstall Flash using Adobe's Flash uninstaller, reboot the system then reinstall Flash from the Adobe site.
Flash uninstaller - http://kb2.adobe.com/cps/141/tn_14157.html
Flash installer - http://get.adobe.com/flashplayer/
My Internet Explorer constantly asks me for permission to run the Adobe Flash Player add-on. I have clicked on "Run add-on" and "Run add-on for all web sites" several times but it still keeps popping up. I have tried uninstalling Flash Player and re-installing it and still get the same problem. I am running IE 8 with Windows Vista Home Premium.