Tech support suggested that this could be due to a grounding problem:
"It sounds like you have a communication issue between your computer and the desktop, this is usually caused by interference from static electricity. It can also be caused by a bad USB cable, a bad USB hub, or a damaged USB port. Make sure that your machine is well grounded, as well as any dust collection system you are using. If the problem persists, check all your cables and run the file with your dust collection turned off. If it runs through, then you need to better ground the vacuum tubing. If it doesn’t you’ll need to ground the rest of your tool.
"Check for any kinks in your cabling, do not coil any cabling. Also, keep the orange power cord free from contact with other cables. Electrical interference causes many of these comm breaks."
The computer and ShopBot are plugged into the same circuit so I believe those grounds should be good, but the pipes from the ShopBot to the dust collector were not ground, so I added some.
grounding.jpg
grounding_cu.jpg
I've now run this profile twice in a row (last one is running now) with no problems. So, just a reminder to ground the dust collection.