FileMaker 12 - yes, it's old. But OSX 10.11.2 (El Capitan) doesn't like to display an FM window well. It will fill the screen, then quit rather than go back to part of the screen. Should I expect this? Or is there a correction involved?
You are definitely swimming without a lifeguard using FileMaker Pro 12 with El Capitan. This combination certainly isn't certified to work and likely won't be. There could be a number of weird behaviors when running anything other than FileMaker Pro 14 (the only version of FileMaker Pro certified to run with El Capitan.)
With that said, I opened up a solution in FileMaker Pro 12 under El Capitan and played around with it a bit and didn't experience anything horrible - not that I would not have if I played with it a few seconds more. Not totally sure what you were referring to when you mentioned "windows" and "screens" but I minimized, maximized, resized and even used split screen and in all cases things appears to work as expected.
I may have accidentally invoked a special menu form - (white letters on black) - and other things such as an attempt at full screen, that made the FM display strange, and partly hidden. The obvious solution is to upgrade to FM14, which I did. That works. Now to see if an FM 14 file will work with an FM12 file owned by a client.