Just a thought, Makerbot already knows what you know, the MAX6675 is
basically to be considered for production no longer available. The
giant hint here is the the schematics for the Mightyboard in the
Replicator has listed the changes and it's a couple of resistor
values. Meaning likely, new versions of the code auto sense the chip
because they have to support the old installed base and work for the
new boards too and not make the user figure out what chip they have.
http://thingiverse-production.s3.amazonaws.com/assets/6d/94/65/9b/90/MakerBot_MightyBoard_REVE_Schematic.pdf
Easy enough to prove, get the breakout from Adafruit, connect it to an
Arduino Mega 1280 or 2560 and load the latest firmware. They branch
the code between models of board so likely the change was made across
the board. You would know in jsut a few seconds if the code works if a
correct temp is reported to rep-g.
Just my thoughts.