Ok, here is what I have discovered and fixed on my CTC printer about this issue. First if you incorrectly level the printer by putting the printhead too close to the glass you will get this issue also. But second it is more then likely the filament is not lining up with the hole for the extruder after passing the extruder gear. If it Is not perfectly lined up you will hear clicking as the printer attempts to force the filament into the offset hole. There are thingys for rebuilding the extruder that will line the holes up. I don’t remember what the numbers where, but look for the parts that allow the use of flexible filaments and you should be fine.
Thank you for all the suggestions! Here the things that I have tried with no change to the regular variation in extrusion:
Slicers: Makerbot and Simplify3D
Drive Gear: removed and inspected, no sign of wear and set screw was tight
Botstep: switched cards around from working axis with no change
Nozzle: switched to brand new one with no change
Bed: leveled repeatedly, tried printing in different places on the bed and different orientations
Filament: 4 different rolls and checked diameter with calipers at several locations
Hotend: Is heating up and no components are loose
So basically everything is working but the extrusion pauses during the print at regular points as seen in the photos on my first post. These machines aren’t that complicated so I don’t know what else to check
Hi, Have you tried increasing the pressure with the screw that changes how hard the drive gear is pressed into the filament? if you have the oldest version of the extruder from Makerbot, it includes a screw at the top and right of the extruder, that increase o decrease the pressure