Don't know about this problem. I have some flickering sometimes too, but not exactly the same one and not all the time.

one thing you can try is using Alt-Tab to go back to windows. then go back to shogun and see if it's still like this. but I doubt that will solve it for you.

best thing to do is posting the same information in our tech forum, the apothecary.

I hope you solve it!

ps1: welcome to the .org Ninjak!!

ps2: YoJimbo, that signature is freaking cool!!