I cant believe I cant figure this out!
I've got 2 text boxes on a master page. I want my text to flow from the first to the second and then autoflow back to the 1st on the next page,
At the moment the text flows from box one to 2 then the next page is created and the text flows from that point on to box 2 to box 2...
What version of InDesign you are using? I tried it on my unit, and everything works fine. I just created File -> New Document (check the Primary Text Frame Option) and the Drag and Drop the Texts from MS word into the first page then everything just works fine. I'm on a Mac by the way CC version.
I'm not completely clear what you are getting, but it sounds like this:
First page-frame 1 then box 2
second page-frame 2 only
third page-frame 2 only (etc.)…
Do I have that right? If so (and I assume you have a single master and not a facing master), are the two text frames on the master page linked to each other? Have you released any frames on the document pages before placing the text?
You should probably show us a screen shot of the master page with frame edges and text threads showing...