I encountered something similar and found that the set screws on the extruder gear wear hitting and getting caught on other pieces in the housing. I had to adjust the position of the extruder gear a little and use only the set screw on the flat side of the motor shaft. Now the extruder seems to be working just fine with the manual controls.

I have a new problem, however, when trying to build something the filament comes out and doesn't stick to the platform, but rather gets dragged around by the extruder. I've been playing around with the settings and so far the setting that seem to work best are temp=215C and extruder Z=0.5, but I'm still having problems. Any suggestions?