Ok, upon seeing the file I got the picture. I’ll use the submitted file’s properties as an example, but the solution is general for this type of situation.
The issue is that the pages are labeled straight from 1 to 137, while the printed aspect of the pages, and how they are listed in the TOC, has the first 24 pages labeled in roman numerals, after which the arabic numerals start beginning at number 1. To make the automatic outline generation feature work correctly it is necessary to match how the pages are listed in the table of contents with how the pages are labeled within the PDF document. Fortunately this is really easy in PDFClerk:
1. Select page 1 to 24 in the page list.
2. Right-click the page list and choose “Relabel Selected Pages…” from the contextual menu.
3. In the dialog “Relabel Pages Starting with Number:” 1 and choose the lower-case roman numeral style from the popup menu, then click OK.
4. Repeat the process for the rest of the pages by selecting page 25 to the last page in the list and relabeling from 1, but this time choosing arabic numerals.
The above process should take less than a minute to perform. The document is now ready to have its outline generated.
In short: The automatic outline feature works fine out of the box when the PDF page labels match the visual page labels. When this is not the case, it is often quick and easy to make the necessary adjustments.