I'm running this game on Windows 7 with an intel HD4000 card and during missions there is a LOT of onscreen flickering/polygons flashing and other general gameplay aesthetic frustrations. I know this game just got re-released but does anyone have any suggestions for me?

Have you tried some basic troubleshooting, such as changing compatibility settings or checking your video card settings? This is an older game and who knows what kinds of irregularity may occur with some of the newer software.

Switching to Software mode seems to help (so far), though it's a rather low resolution. If that's the best solution than it's better than none, though!

This seems to be the general fix that works for most folks. It resolves a lot of issues.

I don't suppose you or anyone else has a solution to raising the resolution from 800 x 600 on software mode?