I'm seeing the same thing here - Yosemite.
Nice to know I am not alone on a desert island.
Happens to me in Mavericks. Bit annoying and sometimes goes away when going to Finder and back or clicking around between applications. Or can be fixed be quitting and reopening. Its just a minor grimlin, but would be nice if it got fixed in the next FM patch.
FWIW, it seems to be not only FileMaker. I had a bizarre bug crop up with the Citrix plug-in the other day that required swapping out applications on Mavericks. Keyboard interactions seem to have mysterious gremlins in the latest releases.
I have noticed this same problem with Join.Me screen sharing, but instead of command keys on the Mac, it is upper case letters. Quite weird.
Yeah. It's almost like the keyboard partially or completely loses focus on the current window or something.
Yes, I have noticed that too because the window won't highlight like an infocus window anymore once this happens.
This is indeed a bit of a pain.
I solved this issue by creating a new shortcut in System Preferences / Keyboard / Shortcuts.
In 'App Shortcuts' hit '+', Select your filemaker application in the drop down menu, Enter 'Layout Mode' into the 'Menu Title' field, then enter the shortcut you'd like to use in the 'Keyboard Shortcut' field.
I set mine to be cmd-opt-L
This is convenient enough for my purposes. Hope this helps.