Hi,
My mouse is really laggy on both my laptop and desktop which are 64-bit Linux machines (Ubuntu 10.10). The mouse catches up with where it's supposed to be in 1 to 10 seconds, depending on how fast and how long I move it. If it is moved slowly it drifts less out of sync. I have tried both 32-bit and 64-bit Cortex Command, which I got from the Humble Indie Bundle. I have tried adjusting the mouse and graphics drivers in Base.rte/AllegroConfig.txt. I have tried low and high values of DeltaTime. I have tried adjusting mouse acceleration and sensitivity in my OS settings.

Any ideas?

The only thing that comes into my mind is that mouse driver polls mouse position at wrong interval.
Is it a gaming mouse(or at least one better than generic, ultra-cheap mouse) ?

Good guess. It's a razer copperhead with the Linux driver from the open-source project: http://sourceforge.net/projects/razertool/
I just connected a logitech mini mouse and that works perfectly. Any ideas what I should do to make the copperhead work?