I was having a similar problem with speed in the extruder. You want to change that in skeinforge under the speed tab (I have my feed rates set to 30). It will not change your start up settings however so when it is done warming up, and purging plastic before a build the speed could still be too quick. To fix this I added a line to the start up file that reads "G1 F200.0" right before my extruder purge gcode. This sets the feed rate to a slower speed. You could also add this into the gcode after it is generated if you do not feel like changing the start file. Hope this helps
