[fysiks]

server.cfg is the config file that is executed when the server starts (it is not, by default, executed on map change). The file designated by the "mapchangecfgfile" cvar is the file that is executed on map change.

So, if mapchangecfgfile is not set to server.cfg, a map change or 'restart' command, won't execute server.cfg and therefore you wouldn't see the changes that you made in server.cfg.

IIRC, there is another default file that is executed by the server itself but I can't remember off the top of my head what it's called or when it's executed.

If you're running AMX Mod X, it executes it's own config file (amxx.cfg) on every map change (or restart command).