The Save As should have taken care of any file difference from being on a Mac.
The Ctrl+G method is completely divorced from the TOC. They have nothing to do with one another.
I have no experience with using Ctrl+G with folio numbering; I do not use it.
How is the numbering for your pages beginning with your Chapter 4 done?
Look at the
pagination field codes in the header/footer by using Alt+F9.