When using stepper-based extruders with makerbot firmware as described at http://wiki.makerbot.com/stepper-driven-extruder you need to transform the skeinforge gcode to translate M108 S codes (PWM speed) into M108 R codes (RPM).
It is pretty easy to postprocess cgode to make these changes (I did it with sed initially) but it's one more thing that you need to remember to do. This is a wee skeinforge plugin to do this operation - the advantage is that then it can happen automagically when you skeinforge, and you can turn the plugin on and off as part of your usual skeinforge profiles. It can also optionally insert an initial M108 Snnn command to set the desired PWM if you're using the extruder controller rather than a stepper driver board.
There are several versions available, depending on which version of skeinforge you use. Choose the version sfNN-rpmify.py where NN is the next lowest version below your skeinforge version.
Rename it to rpmify.py and read the documentation at the top of the file in terms of where to put the file and how to make skeinforge insert it into the chain of modules that gets invoked.
Let me know (lenbok at gmail.com) if there isn't one that works with the latest version of skeinforge and I can update it (or send me your version if you update it yourself and I'll put it here).