The TOC looks perfect in Scrivener, with correct chapter names followed by page number placeholders but when I compile I only get “…” followed by the correct page number. Chapter names disappear when I compile.
As a test, what happens if you go somewhere in the introductory text, and drag and drop an item from your draft folder into the text editor, then compile with that (which is incidentally how you might make a cross-reference). Does the linked name disappear there as well?
I would also do a cross-check with RTF output, to verify whether this is a format problem (PDF) or a settings problem.
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Are yousure your left indent marker is not far in the negative numbers?