Are there any edits made to the doc after you've tagged it? I've seen simple little tweaks make earlier-made tagging go crazy in the past. Simple things that you wouldn't think would affect the tagging. I would also copy or save as, to see if it behaves differently as a different file. Seems out-there, but I've seen all kinds of stuff affect how a document is ultimately tagged.
If there's anything else you can tell us about what might be unique with the doc, do so, please. Good luck!
Do the tags still appear in the tags pane on the pages where Reading Order is missing? If the tags are still there, then I would try closing the document and re-opening. Also, the Read Aloud feature in Acrobat is not a viable method of testing accessibility in a PDF file.