Even with what you, Renob, I had the same problem. It were just happening when installing directly the 2.4 and 2.5 versions. To fix that problem, i first install the 2.0 version with installer. When 2.0 is installed, i run the server search just like you decribe it: it works all the time! I then upgrade the pk3 files to the 2.5 version. And I still got the servers, so I can play! It's a weird problem, I hope that SID will fix it. I hope that thiq trick will help.
See you under Urban Terror!