OpenSCAD weirdness with imported STL
I see you've accepted cmm's answer, but I'd still like to take a stab at the mechanism of the failure based on your comment on it:


  Excellent explanation, thanks. The "WTH" cylinder is centered on the queen piece, and that has a sphere with lots of faces on top. So it looks like the "kink" is inside the queen where the sphere and the base cube overlap, and by accident, my trial-and-error removing of cylinders also removed just the right spot.


My guess is that if you look at the triangle set of the STL file, you'll find the interior of the queen contains the parts of the cube that are inside the sphere and the parts of the sphere that are inside the cube; they may not even be clipped to meet each other properly where they cross each other's surfaces. Sadly there are lots of tools producing invalid STL files like this. The longer cylinder is probaly sufficient to overlap with where the cube and sphere cross, forcing OpenSCAD to break down the model in that region and recompute the mesh where the components overlap. Without that recomputation, the differences likely end up interacting with just the "sphere part" of the STL mesh.

This explanation also seems to be consistent with the description of the thing on thingiverse:


  I much preferred the style of Bauhaus set that TeamTeaUSA's designed, but there was a lot of fiddling with the queen and the knight wouldn't print without supports. So I nestled the queen's sphere further into the body so it would print standing up, added supports for the knight and plated the whole thing.


where it looks like the creator took someone else's STL files and moved parts around to create an overlap, likely without proper tooling that could regenerate a valid mesh.