problem generating a TOC

I have my manuscript folders as seen in the first attachment, marked as doc type structure-based. All the titles are autonumbered with <$R>

I want to prepare a TOC for them, ideally one for both eBook and Paperback but, if not, then one for each.

I’ve tried selecting all of them and using Copy as TOC and then pasting the content into a file in the Front Matter -> Manuscript Format folder. Then I set the doc type to Table of Contents. At compile I also check “Add the front matter” folder.

It looks like this:

Am I missing something? I basically just want my chapters to be numbered and also displayed in a TOC.

What happens is that my numbering for the TOC page is all right but my numbering from the first chapter starts with the number of the latest chapter mentioned in the TOC file +1. How can I prevent it from doing that?