As for Inkscape version, I had 0.91 …I upgraded just now to 9.2 but still same effect.
@afre the reason I want a vector is because I enjoy the look and feel of them. But no offense …if you look at the colours I got, and how yellow the trace ended up compared to the rich reds and greens in the raster, I really don’t think I am demanding the moon and the stars here 
I don’t see why it didn’t reproduce them properly in this mode when without stack scans it does …with annoying transparent spots.
Because the transparent spots do not show up where where is missing and it looks awkward and a bit overly light. A black layer does a better job yet darker than should. I’ll do a tutorial on the method I found solves it.