The main point here is that I believe there is either some bug with cgminer (kinda doubt this) or some major problem with the raspberry itself (possibly USB driver issue? etc) or the wheezy debian distro. I'm using the distro put together by the OP on the thread I pasted above.
I'm sure someone else is also using a pi to manage their fpga miners, so I ask has anyone managed to get it to run reliably without any errors, restarts, etc.?
I've updated the firmware via rpi-update and updated the distro with apt-get update & apt-get upgrade & apt-get dist-upgrade. Problem with 2.10.4 of cgminer still persists.