Hi broody,
after i had read this article from "Tage" i became rather skeptical about the max. usb current:
https://communities.intel.com/message/256066#256066
It sounds not like you can get up to 500 mA current on USB permanently. Maybe the reason for your bad luck?
The question for me is:
Having a good power supply connected at the 5-15V input, what is the maximum current limit on one or both usb (mini breakout board)?