Here you can find instructions on how to set up Linux and WaveForms 3 for Zybo:
http://www.instructables.com/id/WaveForms-Analog-Discovery-on-Zybo/
I don't think it is related to supplying issue. At least I don't see any difference in communication errors when supplying the Raspberry and USB hub separately.
Forcing the USB to slower full-speed seems to be an improvement, by adding dwc_otg.speed=1 to /boot/cmdline.txt
http://www.raspberrypi.org/forums/viewtopic.php?f=44&t=8010&start=75
Most of the cases it does succeed to open the device, configure the AWG and perform an acquisition.
pi@raspberrypi ~ $ python AnalogOutIn.p