I don't have a lot of experience with RepG, but the controls should act pretty quick. You might have a case of motor driver overheating. Which causes the motors to go on/off when the driver shuts on/off because of overheating and cooling again.
http://wiki.ultimaker.com/Electronics_b ... or_drivers
Is the gear turning? Because it's impossible for the filament to really stop the gear. If the bolt is not grabbing the filament make sure you have the pressure screw is tight enough. And the quick release is "closed"
1. Make sure you can push the filament in by hand (if the temperature is too low, it wont print at all.) Just unlock the screw mechanism, and push the filament by hand. If nothing gets out, then something is wrong with your setup.
2. If pushing by hand works, but not mechanically, then look at your filament. Sometimes, the filament tends to get "grinded", this means that the extruder was running too fast or the extrusion was too cold. This can cause the extruder to "grind" the filament off. Just cut the end off, and it should work smoothly again.
3. Turn the adjustment screw a bit more.
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