From another thread:
Are you using the same build locally as you are on the server? Seems like something bizarre is happening just for you. Maybe some file is corrupted somehow? Perhaps you should try a fresh install.
Oops.. Didn't notice this thread had any replies.
Yes both build 40. Linux on server, Windows on my PC. Nobody has said anything to me about this problem since the original issue in this post, so as far as I know it hasn't happened again. If I remember correctly it only happened to me a single time when I was cycling through spawn points testing, I can't remember on which map though.
I wonder if there's some kind of bug with .ent files causing bad spawns on subsequent maps or something...
Next time this happens, type "lastmap" at the console, which should display what the last map was. Perhaps it's caused by a certain sequence of maps.
I will try this if I get the chance.