Check the BG&E forum
on GOG for solutions to most problems.
I can tell you that one major cause of graphical glitches nowadays in BG&E is multi-core processors. Load the game, tab out and open task manager. Set BGE.exe (or whatever the steam version is named) to one core. You'll have to do this every time you play the game.
There is a program called Imagecfg, which can be used to permanently patch an executable to use one core, but you'll have to search for it and how to use it. It used to be distributed with official Microsoft Server Resource Kits. I've only used it with my disc version of the game, and it worked fine. Of course, virus scan anything you download, check against checksums from independent sources, and even then take caution. Note that if you verify the game cache, it will probably overwrite the changes made to the executable.
I can't remember if I also forced Vsync in my video card control panel; it's been a year since I played. In any case, it's probably a good idea, as the game doesn't limit framerate, which could make your graphics card run too hot.