I find the same or very similar happening, and I am using a portable install of MB 3.5.8150 P.
I have removed the "global" option from all key assignments that come up when I type "media" into the Hotkeys search box.
When MB does not have the focus, if the F3 (Play/Pause media) key is pressed, MB starts playing, and if I press it again, MB stops but then immediately resumes playing, as though it is processing both a stop and a start command. The only way to get out of this loop is to focus MB and then use the regular Ctrl+S to stop playback. Pressing F3/media key in MB will stop and then immediately resume playback.
This is annoying because I use F3 all the time in various apps for "Find Next," and if the Fn mod key on my keyboard is not enabled (which can happen easily via a "typo" since it is located next to the Ctrl and Win key), MB starts playing when I try to do a search.
Any ideas? Is it possible that it is Windows that is passing the MediaKey to MB, and that MB is just responding to a Windows command independent of its own settings? I'm using a Surface Pro, with hardware keyboard attached.