Slic3r is using the M106 & M107 commands to turn on & off the fan when required in gcode, but I've noticed that this (I assume this applies just for the Replicator 2) just turns on the extruder fan, not the workpiece fan.
Gcode exported from Makerware shows that M126 & M127 are used for this fan, but there's no way to configure for the change.
It seems to me that the commands are swapped in the firmware, I have notified Makerbot of this, but perhaps it needs to be fixed in Slic3r?
