Are you using a laptop by any chance to connect to the Arduino?
Laptops run from a (mostly) isolated switchmode supply, and can present a weak ~90-100V on the USB connector shell, effectively floating above the unit about to be connected, and then inject a zap into any USB device that is powered from another ground or mains ground before the connection.
It may be that your stepper driver/board supply ground and the PC ground have a voltage difference between them and it's zapping your board's USB IC a bit when connected.
This can happen with a regular desktop PC also depending on where the device's supply ground is coming from. As soon as you mentioned stepper motor on the board side I thought of this possible issue.
You can measure with a multimeter on both DC and AC, between the PC cable USB shell and the board USB shell and GND before connection, you may find a damaging voltage there. It can be fixed by changing your power sources around to either a common ground, or connect the PC USB/connector shell to the board ground with a wire or similar first, then plug in the USB cable after.
Hope this helps!
Marc