I think you're mixing apples and oranges.
VSPAERO can run in a thin-surface VLM mode or a thick-surface panel mode.
The thin-surface geometry generation will have trouble with nacelles.
However, the panel method (your earlier screenshot was like this)
should have no problems.
I've attached a nacelle like I suggest that was extracted from a
Transport aircraft model on the hangar.
As it so happens, it fixes the 'seam' I described, but it still
exhibits the larger problem you noticed. I'm not sure what is
happening here, but I'll try to pass it on to see if we can figure
something out.
Rob
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