This pics are a bit small, you can see better versions at https://goo.gl/photos/YTrp3ihsWZc7Azd96
This closeup of 'Articulated_Piranha_Skeleton' from thingiverse shows S3D on the left, Slic3r on the right. (Object scaled to 66% size, 0.4mm nozzle auto width)
The orange that is poking through is 3
layers deep, and in prints you can often see right through the front and back since all layers are aligned.
The right hand image has the same no-integer-number based gaps, but the VERY next layer (N-1 for an N layered object, similarly layer 2 from the bottom) is rectilinear fill, and provides both a solid, easily bridging surface on the infill to create a flat outer layer - but also closes off holes from the outermost layer.
The top of "KV2-Torreta" from "Tank_KV-2" again from Thingiverse...., sliced at 25% of original STL scale, 0.4mm nozzle auto width
The same issue - you can see gaps in the top surfaces of both, but the second layer plugs the holes in the other slicer.
Alternatively, concentric fills at different angles MAY help, but the issues from bridging non-straight lines on the first of the concentric top layers put down on top of infill obviously leads to hanging strings. I'll do a side-by-side for this and post a pic of that soon,
It's easy to see the drooping on the top section of this Benchy - printed at once with two processes. Please excuse the under-extrusion and stringing, I'm chasing down other problems while writing this one - but the issue has persisted even with these other issues aren't present.
Is there something else I can do to help?