I've got a document and it keeps doing this unaccountable thing -- when I flow in a new story, and let it add pages automatically, it is prone to flowing the pages in this crazy way, see screenshot. ie, it doesn't link to the subsequent page, but to the first page in the next spread, then it links back ot the second page of the first spread and so on. Can anyone account for why this would happen?
I'd suggest that there could be some corruption in the file (if it's just happening to just that one).
You might try saving the file as IDML (File > Save As > InDesign CS4 or Later [IDML]). Then open the IDML you create and try again.
This happens when pages in the document have been moved to move text instead of copy and pasting it.
It also happens that this will change the thread (View>Show Threads) and this you can see how the pages are flowing.
Save a test file:
Delete all the pages except the first page - then the document will autoflow correctly.
Check the pages against the original.
Have you shifted any of the pages to a new location in the document since creating it? If so then that would back up Eugene Tyson's suggestion. If that was not the case then please provide details as to the history of this document's creation.