Are you clicking inside the page, or in the pasteboard area? Are you in Preview mode?
Did you save the AI files with PDF compatibility enabled?
I closed indd and restarted, tried again it seems to be working fine now, bizzare.
Then finally on the last page when I tried to place it was blank again. I noticed the cursor changes when you place. The first 3 pages the cursor had a thumbnail preview of the document it was about to place.
On the final page (I've tried a few times now) it only shows one element of the design, similarly in the place dialogue window when I browse for a file the thumbnail preview is also limited.
So it would only seem to show the same content that is visible on the thumbnail preview.
Obviously when I open that file in AI everything is visible (there is only 1 layer). If I save the indd, close ID, reopen ID and that doc, then I can place the file and it will be completely visible as you'd expect.