Is there a way to find out where the boxes are that the text might be linking to?
Select View > Extras > Show Text Threads
Now select the frames in thread and see where the text is threading to.
If the thread is appearing correct, but text not appearing in a frame, please see if any "jump frame" special characters are causing this.
Such problem would also occur if all frames on regular pages are inherited from master pages, but frames on some pages not participating with master text frame auto flow due to overrides caused for some reasons.