What you have discovered is a new trend in servers for this game. Many servers are using IoQ3 or OpenArena which can produce the errors you are getting. Why are server admins doing it this way? Because IoQ3 & OpenArena are free. You won't be able to connect to the OA servers & only some of the IoQ3 servers, depending on whether or not they use the original pak0.pk3 from a retail q3 disc. With your standard q3 installation you will probably only be able to connect to
RAWHIDE, Wasteland II, Deimos & smokinguns.fr. (There are a couple of others but they are passworded.)
The eventual SG stand-alone will take care of problems like this someday. But if you want to be able to join the most servers right now, and don't mind installing more stuff, read the procedures outlined
HERE.Most people seem to prefer the IoQ3 method.