There are two temporary fixes I know of. I can save the game and begin again. The other fix, oddly enough, is to dive underwater and resurface! I do find that coming into contact with water, or turning on night vision, tends to cause the problem more readily, but sometimes it happens for no reason I can fathom.
I'm running Windows XP SP3 on a Hewlett Packard Pavillion A1410Y, which has an ATI Radeon Xpress 200 card (driver version 8.593.100.0, dated October 2, 2010). I am not using any fancy EDuke stuff like HRP or Polymer. If it matters, my resolution is 1440 x 900.