If it's a map you made, you probably didn't set the transparency right. If it's any map, you're probably using the software renderer for video. Use OpenGL, or if you can't run it, Direct3D.
As said above , try opengl. Software mode iwll just make you feel like your on crack . Also it might be an idea to make sure you have the latest Gfx drivers from ethier ATI or Nvidia Depening on what gfx card you are using
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