The range of settings available through the PTXprint user interface is intentionally limited to try and provide a simpler user experience to meet the needs of MOST users. And it automatically mirrors settings if Mirror Pages is enabled (keeping that complexity away from users). Occasionally you need more control and can specify advanced settings as needed.
Could I encourage you to examine the generated .tex file (see View+Edit tab) to see what is being set, and if necessary you can override those header/footer settings by adding appropriate lines to the ptxprint-mods.tex file (available on the Advanced tab).
% Syntax of defining headers and footers:
RH=Running Header
RF=Running Footer
even=2,4,6,8... (usually the Left page of the spread in a LTR book) - swaps for RTL
odd=1,3,5,7... (usually the Right page of the spread in a LTR book) - swaps for RTL
left/center/right = these are the 3 horizontal positions where header material can be placed.
Within the {curly brackets} you can ask for any of the following to be displayed:
\empty \firstref \lastref \rangeref \pagenumber \book (which is the contents of \h) \bookalt (from \h1)
Note that you can also use codes like: \isodate \usdate \ukdate \timestamp \hrsmins \folio and these can be used in combination with each other too: [\folio]\ |\ \timestamp
Those odd/even combinations cover all the normal scripture body pages. But there are 2 other types of pages:
title=the first page of each book/file in the publication (incl peripheral books/files)
noV=pages that don't have scripture text (intro matter, back matter, glossary, etc.)
So for example,
\def\RFtitleoddcenter{\pagenumber}
means that the center position of odd/RHS pages of the title page(s) of the Running Footer (RF) will have the page number showing
Here is an example from the generated .tex file:
%%%%% Running Header/Footer %%%%%
\def\HeaderPosition{0.758}
\def\FooterPosition{0.083}
%\RHruleposition=13pt
\def\RangeSeparator{\kern.1em–\kern.1em} % what to put between first - last of a reference range
\def\ChapterVerseSeparator{\kern.02em.\kern.02em} % what to put between chapter:verse
%% Even Header
\def\RHevenleft{\rangeref}
\def\RHevencenter{\empty}
\def\RHevenright{\book}
%% Odd Header
\def\RHoddleft{\book}
\def\RHoddcenter{\empty}
\def\RHoddright{\rangeref}
%% Extra Books Even Header
\def\RHnoVevenleft{\empty}
\def\RHnoVevencenter{\empty}
\def\RHnoVevenright{\book}
%% Extra Books Odd Header
\def\RHnoVoddleft{\book}
\def\RHnoVoddcenter{\empty}
\def\RHnoVoddright{\empty}
\VerseRefstrue % Include verses in reference text?
\OmitChapterNumberRHfalse % Omit the chapter numbers in the running header (RH)
\OmitBookReftrue % Omit the book name in the running header reference
%% Footer
\def\RFoddcenter{\pagenumber}
\def\RFevencenter{\pagenumber}
\def\RFtitleevencenter{\pagenumber}
\def\RFtitleoddcenter{\pagenumber}
\def\RFnoVoddcenter{\pagenumber}
\def\RFnoVevencenter{\pagenumber}
Note that you cannot EDIT what is in the generated .tex file, but you can (i) see what is being set, and if needed (ii) change/override the setting(s) by copying the appropriate lines and putting them in the ptxprint-mods.tex file with different {\values} as required.
I trust this helps you figure out what is happening. If not, shout out again...