the newer versions of openarena (0.7.6 and onwards) use sdl, a new way of interpreting input if i've understood it correctly.
the windows version that i tried felt so weird that i keep using the older version (0.7.1). dunno if there's a possible "fix" soon.
i'm not that keen on relearning my movement in the game just yet...
but then again, i'm speaking about windows - your problem might be something entirely different