You really should take this to the jetty-firmware @ groups.google.com which is the forum intended for such issues. These comments are not a support forum. Second, the extruder has to have a temp of 26C or more for the fan to turn on. What temp. shows for that extruder? If you've disabled the extruder (by setting the extruder count to 1), then the fan won't run at all as you've told the electronics that it does not exist. And, it's possible that there's a bug in the code. I strongly doubt that MakerBot ever tested this particular code and this code is identical in Sailfish (since it's the same code).