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I have been printing for a few years now, and recently purchased an Ender 3 S1. I have a strange issue, that I couldn't resolve yet.

If there is a geometric change between layers, then the unchanged parts misalign also. I attach a picture, but try to explain too: A flat vertical wall is looking perfect, but if there is a window in it, the rest of the wall is displaced in the same layers at the bottom and top of the window, then resumes normally. The error is in connection with the object's geometry, not the parameters of the printer. (It is not at a specific Z height) In a calibration cube, this happens at the bottom and top of the Y and X letter indents.

So, I checked the belt tensions, rods are straight, nothing loose, nothing too tight, and the temperatures are steady. I tried 20 mm/s and 50 mm/s, the same result. Not a layer shift, everything else is spot on position. I'm thinking of a slicing issue maybe? Or over/under extrusion? Really out of ideas.

Photo of 3D printed model showing layer misalingment

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This is lost material due to oozing, combined with lack of linear advance calibration. If you don't see ooze/stringing on the outside of your model, it's probably inside, caused by internal travel skipping retractions.

If you use Cura, the Cura term for this is combing. Rather than turning it off, it's best to set the "Max Comb Distance Without Retract" to around 1 mm, and turn on "Connect Infill Lines". This will not add many retractions, but should still avoid all the internal oozing.

If you use PrusaSlicer/SuperSlicer, I believe their name for the same option is "Only retract when crossing perimeters". Turning this off will make it always retract for travel moves.

You'll also want to tune Linear Advance. Otherwise you'll still have inconsistent extrusion thickness that's speed-dependent, and bulging corners.

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