Thanks @Circulus, that would make sense if they were all the same orientation, but they come in mixed.
In the end, the simplest was to create a new document and to set up guides: one to create a 4x6 box and one to create a 6x4 box. This way, I can place the images by dragging either a portrait or landscape box, and I can see in the preview pane which orientation the image is in to draw the appropriate box.
Having an option to automatically rotate to fit the picture frame would have been simpler, but this is not too hard to do either.
Hi Sean, thanks for the reply. It happens to some other documents as well. The files are stored on my iPad by default, although I do keep some on iCloud to test roundtripping to Publisher on my Mac. I have attached the file below for you to look at.
Untitled.afdesign