This bug was assigned to Mian Yousaf who is no longer working with Linaro. https://bugs.launchpad.net/linux-linaro/+bug/709245 - USB Disk IO Slow
Per Andy's last comment: "It seems the issue may be to do with the Panda's hub / ethernet chip idle / wakeup characteristics but since there are no hub registers in there settable from Panda side AFAIK (there are some settable in the missing EEPROM that can configure the hub / Ethernet bridge)"
Is there anyone that is willing to handle? Or provide additional insight? Thanks, Mounir