Luis,
I had that same issue and I had an older serial to USB card. I have seen many issues reported here concerning your issue. Mine were caused by turning on a Halogen light and the next time by turning on a Fluorescent Light, both were on the same circuit as the computer. May also be caused by your USB cable. Each time it happened to me I had to switch USB ports and have ShopBot find the port. Only once did hitting the reset button on the ShopBot controller work. I finally upgraded to the new communications card ($200) and no issues since. Good Luck.
2005 PRT Alpha 48x96
2013 Colombo 3hp spindle
Indexer (converted lathe)
Aspire 9.0