Very odd. So it basically just started doing this one day and now, no matter what layout you use or what tournament you load, it always does it? Would you mind performing a backup of everything and sending it to me?
On the Database tab, press the Backup button, select all checkboxes, then attach the resulting ZIP file to an email to support@thetournamentdirector.net.
I've seen some occasional flashing, but actually on the Settings window and not the Game window. And I figured it had something to do with IE 8, to be honest.