If you’re seeing red flashes during video playback, you might try rebooting your computer. We’ve had several reports of this fixing the problem. Please let us know via the contact form what happens after you do that. We’re trying to get to the bottom of it.
One solution that has worked is to upgrade to the latest QuickTime (and for a Mac version to 10.6.8 of the operating system).
We’ve also had reports that it mostly happens when there is a web page open during transcription, e.g. you have Safari open to a YouTube page. Closing the browser window or quitting the browser will fix the flashing.