I use a Tormach PCNC 1100 at the Tech Shop in San Francisco (I haven't yet pulled the trigger to get my own).
I have had this (or similar) problem. The USB seems really flaky and slow. I usually transfer my programs via USB memory stick. Takes forever to even see the stick. Then sometimes the whole USB bus flakes out (no mouse, keyboard, etc). I have also had it fail to shutdown when I try to reboot. I just end up doing a hard power down once it hangs.
I'm interested in hearing more about this problem and any solutions, too.