That it was missing on some pages tells me that you have multiple header/footers operating.


Header/Footer Settings Recap
Toolkit for Advanced Management of Headers and Footers



Cross-reference fields should have no effect on page numbering unless they are somehow part of the header or footer.

I suspect this was the case. Can't officially confirm it, but the fact that removing the cross references solved the problem, I think this was the issue.

Thank you for the resources as well!