I experienced this problem on my (K)Ubuntu 10.10, brand-spanking new machine.
Symptoms: Any time that I was walking forward (essentially, holding down any key on the keyboard), the mouse would not respond, which made moving around [and playing Minecraft in general] quite difficult.
Cause: If this is happening to you, this is probably not a Minecraft problem. Rather, it is probably "mouseemu", a Linux daemon that handles some mouse button emulation for 1-button mice. If you kill "mouseemu", you should be fine. If you have a normal mouse, you can also just remove "mouseemu" from startup.