Hi Matt,
Its most likely the computer going into a sleep mode or low power mode or an auto back up interfering. want to turn all that off on the computer. You also want to make sure your computer has a large video card (at least 512 mb if you're running large complex files like that). The USB adapters are weak, I wouldn't trust one to running a long complex 3D file. I recommend the soigeneris smooth steeper. They are ethernet connected and have their own power supply so put out a nice strong pulse stream.
https://www.soigeneris.com/ssenc-2-e...stepper-system
Make sure to follow their download and install directions.
ICNC Support