Answer from the Prusa forum: (user: Neophyl)
The best way to debug these is to save your project file (file>save as). That saves a 3mf file. The 3mf contains the model and all your settings. It allows us to slice exactly the same as you and look for problems in all the varied settings. To attach a file to the forum though you need to zip it into a zip archive as the forum is picky on the file types it allows.
With that being said can I ask where you got your snap maker profile from ? I ask as we had another poster also having strange issues with his slicing. Turns out he had downloaded a few profiles and was using them. Those profiles look wrong when I looked at the internal ink structure and contained settings in the printer section that are normally in the print and filament sections. As such it was over riding all sort of settings it shouldn’t do no matter what was set in the print settings.
Also one thing you should know even with a normally working profile that setting a % setting on widths means it is calculated over layer height, not nozzle width. It’s counter intuitive but it is mentioned in the tool tip for those settings. As such when you have a low layer height it will make your extrusion widths also thin. It’s far better to set a specific width for the nozzle like the Prusa profiles do.
The second part with the % instead of fixed widths caused it. Everything was explained in the post you gave me and which i read like 3 times and did not understand what it actually meant.