We have now fully diagnosed the ArduPilot MUX firmware problem, and it turns out there were two problems, not one. The early boards were flashed with the wrong firmware, which was fixed on 1/26, but the boards after that until 2/5 continued to have a second problem, which is that the CKDIV8 fuse in the Attiny45 chip wasn't cleared at the factory, as it was supposed to be. What does the CKDIV8 fuse do? It divides the internal 8Mhz clock speed by 8, so the Attinys ship from the manufacturer with a default clock speed of 1Mhz. Our code, however, was designed to run at 8Mhz, so we clear that fuse to bring the chip up to its full speed.
If you have an affected board, what should you do? Clear the fuse yourself with your AVR programmer and AVR Studio. Instructions are included in this post.
Our apologies again for these teething problems, but I think this time we've squashed the last bug. All board shipping now have that fuse set correctly.