I find that using sections to separate out title pages, from contents
pages, from the body of a document, from appendices etc etc usually
solves these (and numerous other) problems.

To get the appropriate page numbering, do as you did and start the
numbering at 1 for the section you are in. Then instead of the
NUMPAGES field that gets stuck in if you use the header/footer toolbar,
go to Insert on the main menu; then Field; select Numbering from the
types of field; then choose SectionPages and insert it.
That should do the trick...