I still feel AP's "Window" menu needs expanding with other functions (cascade, side by side, etc.) so I don't use it very often and maybe this issue is not related only to the latest beta version...?
Anyway, I had two windows/documents opened and I minimized them. I expected to see them on the bottom of the main AP window (is that right?) but they both disappeared. They were still listed in Window menu but clicking on them did not do anything. I even created a new document and it was invisible too.
To display the documents again I had to use Dock or Alt-Tab from AP and back.