Good people of Adafruit made this tutorial on how to enable your Printrbot extruder to properly work with Ninjafelx filament. All it takes is small 3d printable part and you are good to go ...
Detailed guide:
https://learn.adafruit.com/printrbot-ninjaflex-filament-extruder-upgrade
http://www.thingiverse.com/thing:337267
