I am wondering: do you need to adapt some libraries (those containing Serial, millis etc) for the 12MHz clock?How much?
Why a 12MHz clock? Did I miss something? I used a 16MHz clock with the Sanguino board I built and it seems to run fine.
Nice board, BTW. The Altoids form factor is a great idea.
I changed the frequency definition in the Makefile for the bootloader and in the boards.txt file. No changes are required anywhere else.
So although all the Arduino core functions should work, it is possible that some third party code could have a problem with 12mhz.
One example off the top of my head is NewSoftSerial, see: http://arduiniana.org/libraries/NewSoftSerial/I think it assumes the CPU clock is either 8MHz or 16MHz.Adding support for 12MHz is probably doable but not trivial.
BTW, in deference to Mikal, it's not broken - his software does what it is documented to do.