I think it's because the one not showing is the active window so offering it for selection would be redundant. Try putting the focus on another window and see if the original is then listed.
The files that don't show are hidden. Check Window > Show Window.
I wish I could give you an answer, but I've had this problem myself twice now as well. In my case, a restart of a my machine fixed the problem (at least temporarily). I never did figure out why the files were disappearing from my window menu. It's now been about three weeks since the last occurrence.
For the sake of comparison, I'm running FMPA 14.0.4 on Windows 8.1. The missing files were hosted remotely on the same server. When something was missing, other files from that server were still visible.
We've had the same issue since FM9.
It doesn't seem to be just the Window that we're currently working on, but a whole host of them.
The problem wasn't apparent on Apple Mac, only when we started using FileMaker on PCs.
Did anyone get to the bottom of it?
We're using Windows7, FileMaker 11, soon to be upgrading to FM14.