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I finally found the culprit. I had the option "use adaptive layers" turned on. I would have thought it would reduce the layer thickness on things like the tops and bottoms of spheres, but I didnt think it would reduce the layer height anywhere given I had set the layer height to 0.1mm.
I'm trying to use Cura 3.2.1 to set my layer hight. I load an stl file and have a custom profile with the layer height set to 0.1mm but if I look at the g-code each layer is incrementing by 0.2mm. If I set the layer height to 0.2mm the g-code increments the layer heights by 0.3mm. Ive looked through other parameters to try to find where the extra 0.1mm is coming from but have not been able to locate it.
Do I need to set layer height to 0.1mm less than what I want or is there a setting I have missed somewhere ?