Those types of issues are related to older DirectDraw games when you try running them on newer operating systems like Windows 7. As far as I know, one always encounters these problems when trying to run the Fallout games, no matter where you buy them from.
Fortunately, there are many fixes and workarounds that have been found. For example, check this thread on these forums for how to fix some of the issues:
http://www.gog.com/en/forum/fallout_series/annoying_fallout_2_graphic_glitch/page1 Also, the following link has general advice for fixing ANY DirectDraw game and is worth checking out (the best solutions are farther down the page, so scroll down):
http://blog.macuyiko.com/2009/07/solving-color-problem-red-grass-purple.html Using these methods you can probably get your disc version to work properly. There are some other reasons to consider getting the GOG versions though, including the slew of extras that come with them.