Thank you all for your input.
I have been playing with another model that had problems with 3 holes. It looks like there are multiple solutions to this issue:
1. When uploaded to netfabb cloud, 2 holes were fixed.
2. If I export the STL using 0.001 mesh tolerance instead of 0.003 there is no issue at all. The preview is perfect, but the file is significantly bigger.
3. With a 0.15mm Primary Layer Height is perfect, with 0.2mm no. Change this value by 0.0001 , either up or down, and see if the issue goes away. In my case a 0.2001mm layer height fixed it.
4. Changing the first layer height to either 99% or 101% seems to do the trick too.
PS: Thank you mods for not delaying my posts
English. My. Is. Bad.