If anyone else encounters this problem, a soft-reset will solve it. Wire a PWM pin to the the Reset pin (RST on this board) and set it to low when you wish to reset it:
This is not recommended by the Atmel designers, because it may get stuck in a cycle of resetting, so give a reasonable delay time (>12s) between each reset. Watchdogs won’t work so I would not suggest that. This is definitely a buffer overload, although i’m not sure what is causing it. I’ll update if I find out.
If you need to do other things with the board, I would recommend I2C communication (using the appropriate TVout specialized version) with another board.