Can you check the thermistor? It might be not working in a good way.
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We have also had similar problems. One solution is to repeat the atomic test until you get a smooth clean result. Also use a filament of another color in order to see the residue that you are removing. We have made a fine metal tool with 0.5mm diameter and made a very sharp tip. We heat up the nozzle to 260 and plunge the tool into the nozzle and work it slowly around the edges of the hot-end. I will send you a picture of our tool later. This should be done with caution in order not to damage the inner tube of the hot-end. You can also check the Ultimaker forum. 3D printing forums - Ultimaker Community of 3D Printing Experts 10
Kind regards,
Jaime Cavazos
Ultimaker reseller Greece
Had same issue, replaced the teflon coupler. That was causing this issue and the problem was solved!
This is wat you need → http://3dsolex.com/teflon-replacements 27
I replaced it with this one, and the printer prints like a charm 
Thanks for your suggestion, I’m quite sure that the Teflon coupler is the problem: I checked everything else and my idea it’s confirmed also by the position of the issue highlighted by the Atomic Test.
Agree with Brammezz as I encoutered that before, and solved by replacing a new telforn. Good Luck!
I have been fighting on and off extrusion issues with my two Ultimaker 2’s for a while and this thread may have pointed me to a solution that I had not thought of nor tried. Historically I do a lot of atomic cleans, I have replaced teflon couplers, I keep the extruder gears clean, and prior to my upgrade of both my printers to “+” versions I had replaced the Bowden Tubes with “slippier” versions.
What I had not done was use something like the below to clean, and more importantly, lubricate, my bowden tubes:
http://www.thingiverse.com/thing:190118 23
The difference has been profound. The same print that had extrusion issues printed perfectly with no changes other than adding this filter. I am not sure why I had not done this until now, or in fact if there is some reason that I should not be using it…?
Wow though. Thanks Marc!
Will
That’s a cool suggestion, I’ll try to print one of them and use it 
Cheers,
Federico
I’ve seen this issue before when the nozzle seems to be clean, I’m wondering what your PTFE coupler looks like and if it might be worn out? I change mine about every 4-500 hours but it depends what temps you normally work at. It’s a good suggestion below with poking something into the nozzle. I use a 28 gauge needle (0.36mm), and you can find them any medical supply store. I would also look at the gear box in the back. Sometimes when small bits of plastic accumulating in it can slow the forward movement thus causing underextrusion.
I have a problem that looks like this pretty frequently. It may or may not be the same thing, but usually for me it’s that the nozzle isn’t “primed”. That is, the material has been retracted at the end of a print or when I aborted a print and the start g-code dis not sufficiently compensate for this before attempting to print the first layer.
If that’s the problem, there are tqo solutions:
1. Go into maintenance>advanced>move material and spin the dial until material comes out, then hit cancel and start the print.
2. Change your starting g-code so that it includes a command to extrude a bunch (I call this “priming” the nozzle) before beginning the first layer.
I suppose the other possibility is that your filament tangled… I always forget to check for that first.
by the way, glad the pinecone lamp came out nicely. Sorry for never getting back to you about our g-code analyzer. Unfortunately it only supports rep-rap g-code and does not yet support ulti-gcode.
No problem at all, I’m quite sure that the problem wasn’t the Gcode. I’ll try to order a new Teflon part: honestly, I believe that it is the problem.
I had a similar problem and it turned out to be the extruder. The gears inside the new feeder had begun to push each other apart sideways, down the shafts. As a result, the gear on the stepper motor had moved down the shaft toward the motor, resulting in a loss of movement to the filament. At first I thought it was grinding the filament, but there were no marks - it simply stopped turning the gear.
To fix it, I have applied glue to the shaft of the stepper motor and reattached the gear, in the same position down the shaft as in the upgrade video. As a precaution, I have also glued the bigger gear onto its shaft end.
Hi Jockspice,
Thanks for your suggestion: I have already checked the extruder and, apparently, it’s working in a correct way.
@idamartha @Jaime_1 @SlashDev @jockspice @Clean3D @bramthats @Jamburger @will_kostelecky
Thanks to all of you! Finally, I solved the problem. I disassembled and checked all the hotend. The problem was some PLA wedged between the nozzle and the Teflon.
…And the problem is back, sigh!