LinuxQuestions.org - xhci_hcd short transfer messages with AVR ISPMKII usb firmware programmer and AVRDude

While burning new firmware to an AVR microcontroller using avrdude and an ISPMKII, I get warnings in the message log about short transfers and device resets. My question is - Do I have something configured wrong with the MKII, or is it just the nature of the beast that waiting for a chip to burn causes problems for a USB port that wants to move data out faster than it can be processed?

Code:

kernel: [175958.709973] xhci_hcd 0000:04:00.0: WARN: short transfer on control ep

kernel: [175958.713950] xhci_hcd 0000:04:00.0: WARN: short transfer on control ep

kernel: [175958.716944] xhci_hcd 0000:04:00.0: WARN: short transfer on control ep

kernel: [175958.720927] xhci_hcd 0000:04:00.0: WARN: short transfer on control ep

kernel: [175990.372506] usb 9-1.3: reset full-speed USB device number 16 using xhci_hcd

kernel: [175990.398421] xhci_hcd 0000:04:00.0: WARN: short transfer on control ep

kernel: [175990.399424] xhci_hcd 0000:04:00.0: xHCI xhci_drop_endpoint called with disabled ep ffff8800098a6740

kernel: [175990.399429] xhci_hcd 0000:04:00.0: xHCI xhci_drop_endpoint called with disabled ep ffff8800098a6700

I get similar messages when plugging in a usb/serial convertor, although it works properly. Both the MKII and the serial convertor are connected to a powered USB hub, that is plugged into one of the USB3 ports of my Gigabyte motherboard.

Code:

kernel: [175943.886586] usb 9-1.4: new full-speed USB device number 17 using xhci_hcd

kernel: [175943.912516] xhci_hcd 0000:04:00.0: WARN: short transfer on control ep

kernel: [175943.915531] xhci_hcd 0000:04:00.0: WARN: short transfer on control ep

kernel: [175943.918536] xhci_hcd 0000:04:00.0: WARN: short transfer on control ep

kernel: [175943.919506] usb 9-1.4: New USB device found, idVendor=067b, idProduct=2303

kernel: [175943.919510] usb 9-1.4: New USB device strings: Mfr=1, Product=2, SerialNumber=0

kernel: [175943.919513] usb 9-1.4: Product: USB-Serial Controller

kernel: [175943.919515] usb 9-1.4: Manufacturer: Prolific Technology Inc.

kernel: [175943.922540] pl2303 9-1.4:1.0: pl2303 converter detected

kernel: [175943.950618] usb 9-1.4: pl2303 converter now attached to ttyUSB0

mtp-probe: checking bus 9, device 17: "/sys/devices/pci0000:00/0000:00:1c.2/0000:04:00.0/usb9/9-1/9-1.4"

kernel: [175944.229546] xhci_hcd 0000:04:00.0: WARN: short transfer on control ep

kernel: [175944.232522] xhci_hcd 0000:04:00.0: WARN: short transfer on control ep

mtp-probe: bus: 9, device: 17 was not an MTP device

kernel: [175944.235497] xhci_hcd 0000:04:00.0: WARN: Stalled endpoint

A note on why the USB hub is plugged into the USB3 port - I'm out of USB2 ports, and it's the only thing that works consistently in the USB3 port.

Is it possible that the USB3 port is the problem? If I plug the MKII into a USB2 port it still has the problem with the short transfer messages, whether I use the hub or not.