Additional note: reproduction on the non-PPA version is no longer 100% reliable for me. It worked best with Synaptic opened in the background (it opens maximized; terminal #2 failed on 2 of 2 trials), but opening Firefox maximized didn't expose the bug (1 trial). Still, repeatedly opening gnome-terminal, maximizing it, and repeating failed when the click on terminal #4's titlebar brought terminal #3 into focus instead (1 trial).
With this new knowledge, I retested the PPA version. I couldn't get it to fail, even opening firefox or synaptic, followed by 13 terminals (1 trial each). Still working for me, then.