So I tried to print a model with a 2 mm thickness main area, and a couple 4 mm parts that stick out.
Instead the 4 mm is 3.05 mm and the 2 mm is 1.07 mm (0.042 inches measured with a caliper).
The only physical thing I changed was the nozzle from a 0.4 mm to 0.2 mm.
I changed to Ultimaker Cura 4.1 (from 4.0) and entered a 0.2 mm nozzle size in the settings. Just as before with the 0.4 mm nozzle, I used a 0.1 mm layer height.
The X and Y dimensions are good, and the screw holes line up perfectly.
I auto homed and used the bed leveling mechanism built in one many times.
Any suggestions why the height of the printed part is too small?
I don't have the model with me, but this is an example (without the holes):
I am manually using the GUI of Ultimaker Cura, not the slicer engine embedded in another program or from command line.
Do I need to increase the filament temperature up from 200 to have the filament liquid enough to flow through the smaller tip?
The old models are rigid, and the new ones bend because it is so thin.
update 6-10-19
I re-installed 4.0 to no avail.
I think the problem might be related to the filament feeder because otherwise there should be filament everywhere. I am going to try different filament temperatures to see if that changes anything. Trying 205. Unless the feeder motor is damaged.