Progress update. The board is currently clocked at 256 and its mining at 3.6 GH/s. See https://bitcointalk.org/index.php?topic=198489.msg2712124#msg2712124

WU: ~55/m. Error rate is really low too.

I still don't know what happened. I mentioned periods of total inactivity that I was noticing in the log file. I tried to debug it and realized that there was some kind of locking conflict while writing to the USB. I didn't change anything, was just trying to log additional information. Added a few lines of code to log in logging.c and miner.h. Tried to run again, and there were no conflicts anymore. Will look at everything again tomorrow and try to pin point the issue.