Fwiw, this only happens when you use the mouse to select View > Full Screen/Exit Full Screen -- the keyboard shortcuts don't exhibit this behavior. (I was trying to replicate and couldn't until I used the mouse.)
There's a similar bug I've been meaning to report, perhaps they're related -- when you have two windows open in (simple) fullscreen and close one of them, the OS X menu bar reappears for the remaining open fullscreen window(s). You have to exit and re-enter fullscreen (cmd-ctrl-f x 2) to make the menu bar disappear again.
To replicate this bug:
0. ye olde "use_simple_full_screen": true
1. open two windows (cmd-shift-n x 2)
2. fullscreen both of them (cmd-ctrl-f, cmd-`, cmd-ctrl-f)
3. exit one window (cmd-shift-w)
4. menu bar shows on remaining fullscreen window