I can't say for certain, but one issue I've seen in other Quake3 Engine based games, is that on occassion textures from one map can "sometimes" cause textures from gamedata/base (or in this case rtcw/main) to fail loading, thereby causing untextured brushes to appear in-game.
This would most commonly happen when a map was ported over from one game to another, such as in from ET to RTCW or vice versa though it has been known (in Star Wars: Jedi Academy for example) to happen simply because the textures of a custom map conflict with one or more of the default game textures. I never did get straight answers on the exact nature of these texture conflicts, I would assume their filenames would be nearly irrelevant as for the most part they were given their own "mapname/textures/mapname_texturename.jpg" type path/name.
This may not be the issue you're having but if this started after a recent addition of maps to your main directory, I would suggest removing them to see if the textures return. If so you may have to re-add the maps one by one to narrow down the culprit.
Sorry if this doesn't help any or just comes off as the ravings of a deluded fool.
heh.