Ok, because screenshots just don't work I've made a video of the flickering problem. It's 25meg - smallest I could get it with reasonable quality I'm afraid, and I have no youtube account, so you can download it here:
http://www.mediafire.com/?4ov2ga49jhsugbu
Hopefully this helps someone figure it out! It's starting to grate but I don't want to drop MO as it has the nicer torpedo loadout screen etc.
