If it's something like Ubuntu Hardy, you may have Pulseaudio enabled, which is
not recommended for ioquake3 (see
Why is my audio crackling / distorted under Linux?).
\s_info in the console should tell you whether you're using OpenAL or SDL.
It's v8.4.1, which is Hardy. I don't have pulseaudio in use - it might be installed. I had openal disabled in the in-game option, but s_info told me it was using it. I disabled it using one of the other suggestions above and that seems to have fixed it - s_info now just returns some info about samples.
I am using compiz. Is the suspicion that this might be involved with the mouse icon problem? I could try disabling it. I'm not sure about the serverpatch suggestion - for one thing I don't know what to install or how, and I'm running a client, not a server.
I've not consciously installed libopenal0a, I believe. This is for the audio though, right?
The mouse problem is weird - sometimes, in the middle of the game, the mouse icon will come to life and respond to my mouse movement, meaning that although the keyboard still works and I can move around as before, all mouse movement to the game is ignored, so i can't turn and point and fire at anyone. This lasts for up to 10 seconds, during which sometimes the previously full screen game becomes windowed. A few seconds later the game continues as before in full screen mode.
I'll try turning off compiz and see what effect that has. I'm a bit of a linux newb - this Acer box is my first (serious) attempt at using it. I really like it, but it's still fairly alien to me!
Thanks for all the advice so far.