9600,
I did this exact thing this morning, and in fact the network worked fine (and the usb after some fiddling around)...some power cycles and such.
So 'it was working' and now after I 'shutdown -h now' then powered it down, and disconnected all cables from Parallella the USB has been back to giving me the -99 errors.
Just as I was typing this message I was trying something else...with the same hdmi kern/fpga installed. I powered the box down and connected my powered usb hub, only this time I didn't power the hub. SO power to the barrel connector on the Parallella and no power connected to my powered hub. And I see this:
"Welcome to Linaro 14.04 (GNU/Linux 3.12.0-g0bc9c3a-dirty armv7l)
* Documentation: https://wiki.linaro.org/
Last login: Wed Dec 3 22:17:53 2014 from 192.168.3.12
linaro@linaro-nano:~$ lsusb
Bus 001 Device 003: ID 1a40:0101 Terminus Technology Inc. 4-Port HUB
Bus 001 Device 002: ID 1a40:0201 Terminus Technology Inc. FE 2.1 7-port Hub
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub"
So now I plug in an RTL (tv) dongle and lsusb says:
linaro@linaro-nano:~$ lsusb
Bus 001 Device 004: ID 0bda:2838 Realtek Semiconductor Corp. RTL2838 DVB-T
Bus 001 Device 003: ID 1a40:0101 Terminus Technology Inc. 4-Port HUB
Bus 001 Device 002: ID 1a40:0201 Terminus Technology Inc. FE 2.1 7-port Hub
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Notice the Dongle shows up. This is still with the powered usb hub (UN-POWERED).
I've heard of usb ports that don't like to see any return voltage coming from powered hubs at init time. (dunno why really, seems some things are ok with that and some aren't)....
Anyway...that's where I am with this now.
1.) the network has started up every time with the HDMI kern/fpga.
2.) the usb has started up 2 times now with the same as above.
Hope this helps? And thanks for you response.