I've upgraded my makerbot rep2 to the lastest 7.7 sailfish firmware. now when I cancel a print, the printer attempts to send the bed too low resulting in nasty chatter as it bumps the bottom of the screw (no end-stop there). if the print finishes normally, the bed lowers to the correct height without bumping.
I believe that action is actually controlled by the firmware, and not the software. So perhaps you did something wrong when loading sailfish and didn't correctly set travel distances.