Major pagination issue – any help or troubleshooting ideas appreciated

I’ve got a serious pagination bug with InDesign (tested in both CC2014 and CC2015). Apologies for long post, but it’s difficult to explain.

I lay out reports from Word (2010, .docx files) into InDesign chapter-by-chapter in a Book, using a template (Styles and Master Pages) I’ve built from scratch. My workflow after placing each Word chapter file into InDesign involves systematically deleting each imported Word Paragraph Style and replacing it with its InDesign equivalent. I then do a general clean up, including applying Style overrides for anything that didn’t match properly.

With a recent report, I noticed that while going through some chapters after Style matching, some pages/Text Frames were doing something weird – the footnotes at the bottom of the page were aligning themselves relative to the top of the page (as opposed to near the bottom of the frame’s text) by the distance specified as the Minimum Space Before First Footnote (in Document Footnote Options, in my document 10mm) – leaving massive white space.

Screenshots here of the bug:

Chapter 3 example: https://imgur.com/NRLs3aS
Chapter 4 example: https://imgur.com/mOdWEpx

Screenshots here of what the respective pages should like:

Chapter 3 fixed: https://imgur.com/c50UbiF
Chapter 4 fixed: https://imgur.com/PfyqEbw

Nothing in the bugged out text frame can be selected by the Type Tool. To *temporarily* fix the problem, I can do anything that refreshes the view of the page, like forcefully re-applying a Paragraph Style before the offending page (holding Alt and clicking on a Paragraph Style), or going into any settings/options and modifying a measurement that affects the entire document.

This makes me think that the problem is a bug, not anything wrong with my Paragraph Styles or something I’ve created in the document. It might be something to do with the original Word file, but the same problem has happened with different Word documents based on different templates.

Back to my InDesign workflow, when I continued cleaning up the document, sometimes the same thing would happen to the same section of text again and I’d have to go back and do that tinkering until the pagination was fixed.

However, this didn’t end up being a viable workaround. While I could get each chapter file looking like it was supposed to with no messed up pagination/footnotes, after I generated the table of contents, it re-made the same pagination error in the exact same spots.

And the HUGE problem with this was – the page numbering in the TOC referenced the incorrect pagination from the bug. This happened near the printer’s deadline with a recent report and needless to say it was a nightmare of manual page numbering.

I thought it might have been an InDesign CC 2015 issue, but the same problem happens with CC 2014. I’ve gone over all the options in my Paragraph Styles and can see nothing screwy with Keep options or anything else, nor with my Document Footnote Options. This problem seems to happen randomly once or twice in some documents and not others, but I can’t replicate it or find a pattern. My best guess is it’s a bug with Footnotes. I’m really stumped.

Any perspectives on this would be greatly appreciated or the experience of anyone who has encountered this same issue. I’m pretty desperate to get this resolved before a slew of reports later this year.