The foreground application isn't always the active application - why?

I've noticed this several times. The foreground application quite often doesn't seem to be the real foreground app. For example, I switch from FileMaker to iTunes and type a short string to locate an artist - e.g. 'beat' to bring up Beatles in the Artist list, but it navigates to The Eagles instead. So I shrug and retype and it goes to The Beatles ok. A little later I switch back to FileMaker to find an error message "Please tab to a field before typing" - yet I hadn't done anything in FileMaker. It seems the first character I typed in iTunes was actually received by FileMaker before iTunes took the rest of it.
And just now - I clicked Preview in the Dock and the menu bar changed to show I was apparently in Preview. So I pressed Cmd-Q to quit Preview but Safari quit instead (I had been in Safari, then Finder, then switched to Preview). And no, I hadn't hit Cmd-tab accidentally while trying to press Cmd-Q.
What is happening? This seems very weird. I haven't tested it, but I'm wondering if switching apps via the Dock MAY be a common factor here?

Weird. Are you noticing that it happens mainly when you switch apps via the Dock? And just as a long shot, do you use FileMaker Pro, and if so which version? (I only ask because I haven't noticed this happen in other user accounts where I don't use FM).

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