Also if you model is good you can uncheck all the "fix horrible" checkboxes as they make a good model print badly.
Thank you very much for your answers. I really never looked at my models in layer or x-ray mode, because all the OpenSCAD models just worked.
Experimenting some more, it seems that FreeCAD creates usable STL files unless you add fillets to the model. I'll have to avoid these for now.
Also never ever print a part without looking at it in Cura layer view. If you had done that you would have seen the problem before writing gcode to SD card. Also use the xray view in cura and it shows problems with your model in red.
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