Thanks for the reply. I think I have resolved the issue, or at least fixed it in this case.
I started by loading the STL back into my CAD program, and I couldn't see any obvious issues. I also checked the X-Ray view in Cura as per your suggestion, but couldn't see anything wrong.
It turns out that it was due to having a solid "roof" on my support structure. When I changed it to a rib design, this strange single initial layer went away, and Cura interpreted the area appropriately as per the settings.
The images show the 3 layers in question - no strange infill.
From your photos is looks like that first 'fake' solid layer is too wide for the top of the arch and really is not supposed to be there.
My guess is there is an error in the .stl file. If you look at in in x-ray view in Cura are there any Red areas? Those would be issues with the model.
You can test your STL file in some web-based STL repair tools, like MakePrintable, to see if there are any issues with it.
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