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Now this doesn't have anything to do with my graphics card. This only happens in Minecraft. I use Windows 7, the problem starts and stops randomly. It only affects in game, not the menu, only the part where you actually run around.
I played around with the options, but nothing seemed to fix it. The colors turn from creepily shaded red and blue grey, and colors that look like an acid trip. The shading freaks out and teleports to different sides of blocks in a pattern that looks almost like the biggest QR code in the universe. If I dig down one block, its red and blue. This isn't caused by the 3D anaglyph; I always have it off.