Strange Jamb

[printbus]

I agree that it could be retractions that are causing your problem. I know I have ran into that. I can't speak from exhaustive personal testing, but I had read that direct extruders shouldn't usually require more than 1 or 1.5mm retraction so that might be something to try. Since you're using slic3r, you could also try increasing the setting for minimum travel after retraction to reduce the number of retractions.

FOLLOWUP: If you're using 3mm filament, I would think this is especially true. A 3mm length of 3mm diameter filament seems like an large volume to retract. To evaluate this for yourself, raise the nozzle off the bed and extrude 3mm of filament. Observe how much came out the nozzle. Do you think you should have to pull that much volume back out of the hot end when you're lifting the nozzle for a retraction?

When you mentioned 3mm retraction, I thought maybe you were using Cura since IIRC it defaults to 3mm. I believe it does this since the Ultimaker that Cura is mostly developed for is a Bowden extruder and considerably more retraction is necessary due to hysteresis in the Bowden tube. Cura also has a setting for minimum extrusion before retract that can help reduce retracting the same section of filament. I currently run Cura with retraction distance set to 1.2mm and the minimum extrusion before retract to 0.5mm. This has been a helpful combination, but I don't think Slic3r has the equivalent of the minimum extrusion before retract setting.

I'm not trying to influence you, but you asked for input and you haven't received much. One of the things I disliked about Slic3r (especially on versions newer than 0.9.9) was the way it seemed overzealous in going back over things to touch them up with just dabs or short extrusions of filament. Too many of these in a row and you're setting up for chewing into the filament. I was amazed at the difference in the number of these hops when I started comparing Cura and Slic3r results in a gcode viewer, and dumped Slic3r shortly after.

That said, even with Cura I've learned to look at the layer-by-layer print moves in a gcode viewer for anything with the potential for small amounts of extrusion. If necessary, I'll go back and reslice with retraction turned off in order to keep the hobbed bolt from repeatedly turning on the same length of filament on these prints. The avoid crossing perimeters setting helps minimize issues with stringing. This is another area where I personally think Cura is better at managing perimeter crossing than slic3r.

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I have also had filament stop extruding if the nozzle temperature gets too low. This has normally happened when I'm just experimenting with a lower print temperature or messing around with a print cooler and end up blasting the nozzle with more cold air than the heater control loop can deal with. With the nozzle off the bed and motors disabled, you should be able to get a feeling for how easy it is to extrude a particular filament by manually rotating the large gear or releasing the guidler and just feeding the filament manually. As you lower the temperature and start to feel an increase in resistance, up the temperature by 5-10 degrees as the setting for that filament. At least that's what I've read as far as one way to determine the proper temperature to use for a particular spool of filament.