If all visual effects are turned on for Ubuntu (running the defaults ie. Gnome) then the clock keeps appearing on the screen and it doesn't allow me to click on any buttons. As the problem disappears when settings are turned down, this is not a a major issue.

this seems to be a bug in ubuntu in general, not exclusive to this game

Can you give us some more details about your system? Could be a graphics driver bug, it wouldn't surprise me if Ubuntu has included a broken driver.

Try disabling Compiz if you have it enabled.

It does the same thing on my system also. It must be a Ubuntu bug, as the same thing happens with UT2004. If I turn off the desktop effects, everything runs fine. It seems to do the same thing whether I use an Nvidia or ATI video card.