I don't use a makerbot or their software (solidoodle 3 + repetier), so I can't be too specific - but I think this may be an issue common to FFF printers that can be dealt with.
I'd suggest setting your first layer thickness back to 0.2mm, then let the subsequent layers continue at 0.1mm - trying to print the first layer too thin makes it really fussy about your z height and how level the bed is.
If you don't want an 0.2mm layer at the bottom of your part for any reason, you could print with a raft to eat up that first layer.
SD3. Mk2b + glass, heated enclosure, GT2 belts, direct drive y shaft, linear bearings, bowden-feed E3D v5 w/ 0.9° stepper
Smoothieboard via Octoprint on RPi