Sometimes it does regrab fullscreen after a few seconds - and sometimes it doesn't, continuing to run in windowed. I've recently set up a "debug server" so I can query the various flags at runtime, and I'll see if it re-occurs.
The "sometimes it doesn't" sounds like a real bug - other platforms (windows and mac OS X for me anyways) go back into exclusive fullscreen mode when the app becomes active again. On most windows machines I've tested on, it does take a few seconds for the process for that to complete, and in such cases I believe the delay is just an exclusive mode thing and out of SDL & pygame's hands. However, I've never seen it not go back.
When it doesn't regrab fullscreen, I can't seem to nudge it in the right direction as an "end user" (like changing focused window).
again, sounds like a bug, probably an SDL one.
I don't suppose you can get a similar problem with your systems alt-tab (or equivalent)? The reason I ask, is the whole SSH'ing in and then running something to take fullscreen part of things sounds like an uncommon usage case to me and I'm curious if the cause of the problem here is specific to that behavior.