Found the answer from Carl Schartz back in December:
"I found the answer. The object I'm dragging in to the portal is a "popover" which has a portal inside it. Portals can't contain portals so Filemaker only makes it sit on top."
You just have to tweak the position a couple of pixels left or right. Make
sure it fits within the portal vertically. Leave a pixel above and below
Sent from my mobile device... Please excuse typos.
If you want to have a portal in a popover in a portal you can 'spoof' it with a popover outside the portal and use the button to open the popover and set appropriate conditions to make the portal display the correct related recods. Its a little bit FileMaker 6 in terms of hackery but it works ok.