Do you have your program set up for a Makerbot Rep 2 WITH sailfish firmware installed ? I know you should already have it set up for printers that have the Makerbot firmware. Thinking of updating the firmware TO Sailfish anyone have any thoughts on this as well ?
S3D is pretty firmware agnostic: It spits out .gcode (and in the instance of Makerbots & their clones, converts this to .x3g) for consumption by the firmware: I have a custom built bot running Marlin, a Rep1 and Rep2x both with Sailfish, but use S3D to slice & output for all of them.
Bots:
Makerbot Replicator 2x / Sailfish on Mightyboard
Custom C-Bot / RepRap Firmware on RADDS
Custom Tevo Little Monster / RepRap Firmware on Duet