In 2.4.2 there is a tiny (already fixed in svn) bug that makes fog affect flags in CTF too much.
To fix it as a player, build a current svn build of the engine.
To make life easier as a server admin, you can install this package:
http://www.informatik.uni-frankfurt.de/ ... lagfix.pk3
and apply the included diff to your game sources, or if you use 2.4.2's unmodified game code, extract its progs-flagfix.dat to progs.dat on your server.
Background: the bug actually is fog applying wrong to any model that is scaled using the "scale" property in QuakeC. The engine fix fixes the fog equation to work right for this case. My flagfix pk3 is a temporary solution that contains scaled flag MD3 files, so they no longer need to use this scale factor and display right.
Scaling a MD3 file seemed to be not easy, I had to write my own Perl script for doing that. In case anyone needs it, the MD3 scaler script is included. It scales a MD3 with animations, as opposed to Blender and Miklshape, which lose animations when importing a MD3.