Awesome. That is indeed what it turned out to be; I had a transport on autoexplore, stuck in enemy territory, and once I disbanded it, my game continued.
BTW: Transports? Broken. Harbor? Pretty much useless. How so? Transports, on autoexplore, go much slower (in terms of how fast the game is running) than anything else. I'm not sure what the autoexplore algorithm does with transports - and it's generally pretty sucky in otherwise awesome games such as GC2 - but there appears to be no logic whatsoever in where it goes. This is in addition to how much it slows down the game. And harbors can only build transports? No food bonus, no ability to create warships, etc? Not really worth building.