Thanks again for bringing this to my attention, surprising no one else has reported this. Could just be no one uses Linux all that much for gaming.
In the meantime perhaps playing in windowed mode, leaving fullscreen (F11), may help work around that.
I have some ideas now for a patch, but I'll have to test using my Linux CD since it's not installed. The next patch comes out before Halloween so hopefully I can get it fixed before then.
I greatly appreciate the time you took to report this, it could have gone unnoticed for so long