1. Which Makerbot printer,
2. Which firmware in the printer,
3. Which version of RepG, and
4. Which Machine > Machine Type (Driver) have you selected in RepG?
This is exactly the behavior you would see if
a. You are using Volumetric 5D gcode with older firmware,
b. Using non-Volumetric 5D gcode with newer firmware, or
c. Are using the correct style of gcode but have the extruder axis "inverted" and
it's turning but in the wrong direction.
Dan