I'm running Vista and I seem to have fixed the worst of the graphical glitches in this game by turning of AA, however I still have one rather annoying problem. When I start the game I get a flashing line at the very bottom of the screen (sometimes it the whole screen, sometimes just part). I think it the Vista taskbar trying to draw itself over the BG&E screen. Has anybody else experienced this? Does anybody know of a fix?

hmm , i never experienced this one before but if its the taskbar trying to come through , why not try to hide the taskbar :)

i got that when i was running rocket dock, it would try to show up behind BG&E and annoy the crap out of me, i turned it off during the game, which helped, your only option might be to shut down any and all other windows you have open, perhaps even the side widget bar if necessary

So, it's a little academic now since I finished the game last night, but, I always close the sidebar before starting any game for two reasons, one, the live widgets still update themselves even if I'm not looking (i.e. they slow things down) and two, I have had it come through on other games as well. So the sidebar isn't the issue. It's closed before I start.
As the for taskbar, it's set to auto hide, so I don't know what else I could do with that.
I have also been interrupted and kicked back to the desktop by my virus scanner while playing BG&E and when I try and tab back, I now have a flashing windows chrome around the top of the screen! Very annoying.

I have the same problem. When I start BG&E, Vista's Start button and two icons in the systray (Kaspersky and the network connection indicator) are flashing like mad. I solved this by making the taskbar not always on top.
BUT...
This does not help the problem with Alt-Tab. Once I used this during the game to check an incoming e-mail or whatever, the whole screen borders flicker as if constantly switching from windowd to fullscreen mode. This is super-annoying, even more so than just the few icons on the bottom flickering.
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A FEW DAYS LATER...
I noticed the flickering is just at the top and bottom parts, not the whole length of the screen's vertical sides. This let me to the idea of changing the solution, and it actually helped. So no more 1280 for me but at least 1024 works w/o the flickering.