sphinx documentation contents should have depth of 3
(I base this on the generated docs on the site.)
Right now, it has a maxdepth of 2. The markup constructs section itself has a depth of 2, so on the contents page 3rd-level headings are flattened together with the 2nd-level ones.
For example, "Object description units" is displayed with the same level of hierarchy as it's parent, "Module-specific markup".