Here is the .3dm file.

As shown in the video clip, I swept the initial shape using the angled vertices using the upper and lower closed loop rails (the bottom one dropping in the z axis in a subtle curve).

The upper loop "opening" is the where the problems are.

After creating the outer shape, I used "planer" to close the opening using the edge formed by the swept shape. So in theory I would think/assume that the now closed "opening" would be seamlessly filled with the planer created face.

I then "joined" the outer shape with the filled planer face of the "opening" to make a single object.

Shelling (or even offsetting) that object by a sizable amount those anomalous gaps or openings are introduced in what should (at least the assumption at any rate) a fully filled center face.