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are your sync options set correctly? can you post a screen shot?
I had deleted the folio frames completely on that particular chapter and recreated with new frames and got the output correctly with sequence folio. But couldn't able to find difference on the frames.
I had set the Sync options correctly - no issue with that.
Had the same problem – drove me mad. Only one or two chapters in each book were effected. And because we did not spot this, we were selling books with the same page number all through a chapter.
I found a solution that works every time, and it is quite simple. The problem lies in the Master Pages section.
The solution is to create a new Master Page (but not copying the previous Master). Copy details from a Master Page that works! Make sure the new Master has the same dimensions and indents as the old one.
Then change all the pages in that chapter to the new Corrected Master. (A global change to all pages – easy to do).
Presto – you should have proper page numbering in the resulting pdf.