As signage suggested above, my first thought would be that the computer is set to some power usage settings that is disconnecting communication with USB devices after idle for so long. What is your OS, and I can help walk you through how to change your settings to "High Performance" or "Always On".
The next possible cause could be the length of the USB cable as going above 15 feet length can cause communication errors.
I had the problem until we set our production manager up on a "spooler" we have two older Summa plotters that use serial ports and two newer plotters that are USB. We switched to mac's (no serial ports) and ended up setting up two PC's as spoolers - two plotters on each. We haven't had any cutter not responding messages since. We never did figure out why, just kind of worked around the problem.