The problem it turns out, was with the Extrusion Hold setting in Sailfish.
This experience has convinced me to seek out a new slicer. Unfortunately there are very few that export to Makerbot's X3G format. I tried out MatterControl, and while it does output an X3G file, that file is not suitable for use on a Makerbot by default. The file I tried didn't even wait for the build plate or nozzles to heat up before it started printing. Plus MatterHacker has a really unpretty interface that I don't like so far. I'm keeping my eye out if anyone comes up with a fix for the X3G for MatterControl, and in the meanwhile saving my pennies to buy Simplify3D.