I am having the same problem and I've figured out how to repeat it. This happens when the default layer height is not the same as the layer height selected in the drop down box, then you switch print configurations.
For example, I have a Z-hop and a non Z-hop print config both with default heights of 0.2mm.
If I select Z-hop, then select 0.1mm under quality, it slices at 0.1mm, but if I then select non Z-hop but DO NOT TOUCH the quality, which is still displaying 0.1mm, it will slice at 0.2mm unless a re-select 0.1mm from the dropdown.
This bug has bit me multiple times and its really annoying, please fix!