This is weird, it just came up today, so I suspect it may be related to FM16 (although maybe it's related to Sierra, which I just upgraded to).
Product and version FMPA 126.96.36.199
OS and version MacOS 10.12.4 Sierra
Hardware iMac (Retina 5K, 27-inch, Late 2014)
I have multiple windows open from multiple local database files.
I can navigate as normal between the windows using the Cmd+` shortcut (command tilde), but when it gets to a certain one this shortcut stops working. I can click on another window and switch between windows, but when I get to that same one, it stops.
If I close that window, the last window I had open before it then becomes the one that the navigation stops at.
How to replicate
I wasn't able to replicate the issue.
I'd been troubleshooting some import scripts and I had (different) files open simultaneously in FMPA15 and FMPA16.
Maybe it was a one-time issue. If it happens again and/or I can replicate it, I'll report back.