that seems very strange to me.
After testing USB cables (with and without ferrite chokes), Filters and reading application notes
for a couple of months my only solution seems to be a good USB Filter
like the Wuerth EPLE + blocking the USB shield to pcb ground with
a 1M Ohm resistor in parallel with a 4n7 Cap.
To stop and restart the Software had no effect (and if so it would have surprised me)
vy 73`s de