I have one machine running Fedora 13 x86_64 and the Quake3 from the repo (ioq3 1.36). Another machine is running Windows XP and is running the latest version 0.8.5 downloaded from openarena.ws.
You shouldn't install the ioquake3 binary on Fedora, but the OpenArena binary. If there's no such RPM package in the repo, then you can always download the version from the website. I think the protocol numbers are hardcoded into the engine.