I had this same problem using the version 3.0.1 and also the newer version 3.1.1 from
PYNQ supported boards and PYNQ pre-built images | PYNQ.
Curiously, it didn’t seem to effect using the PYNQ servers over the USB3 cable, but I did not do any excessive testing.
After going around with people at RealDigital, I finally got the answer: there’s a new USB chip I think for the usb3 port, and RealDigital had to make a patch to 3.0.1. Here’s the patched image:
It’s a patched 3.0.1 image. When RealDigital ships a new board, the image on the SD card that comes with it will have this patch. As of last Dec, the images on the PYNQ.io web site does NOT have the patch (although maybe they fixed it by now).
I guess you will need their patch, so maybe contact RealDigital and see if they will help. Good luck!