USB Mouse/pendant jitter

So I'm running vanilla LCNC - current release on Wheezy, everything up to date. The system is a new Gigabyte board running a Skylake (I think) Core I5 CPU with a Mesa 6i25/7i76 setup. Everything has been great except, I'm thinking, the iMach 4 USB Pendant I bought. It frequently misses axis changes and the scrolling performance is erratic - its cost me a few cutters.

Fast Forward. I've noticed when I let my CPU run (like overnight) no LCNC - just a computer and Linux - the mouse is very jumpy the next day. Not unusable, but definitely not smooth. A reboot clears things up. Whats more, after a reboot the USB Pendant works great! Quick switches between axes and smooth scrolling. But I don't like to reboot computers needlessly, and I would like to know whats going on. This system should be more than up to the task, and is until the bit-rot sets in.

Is there a Linux system setting I'm missing? Maybe a BIOS setting? My experience is dated back to when it was spelled Unix so I'm not very current. Looking for some direction to explore.

p.s. FWIW Linux does not like to reboot with the USB Pendant plugged in; I need to attach it after Linux is booted.

Thanks Andy. Yes, I think its a Linux problem - just hoping someone here might have come across it. I think I learned that the bad mouse behavior starts after the screen saver runs. Maybe get a chance to figure that out today. Obviously don't need a screen saver...