Everyone, there is a much easier way of doing this:
There's a mod for editing the resolution of the game (must be version 1.02 or higher)
Simply download the zip file: No Mutants Allowed :: Files
Extract it on a folder of desktop.
Read the f2_res_README and follow the prompts.
If you have followed directions properly, you should adjust the bit depth of the game from 6bit to 32bit.
This fixes the problem with incorrect colors, as stated by OP.
Please feel free to PM me if you have any troubles.