The island of Flores remained an island during the Ice Age too.(From all that I can find)
Something else I've been think about. The Toba eruption supposedly killed almost all humans on earth 75,000 years ago...in fact, the NG special I watched last night said that the only survivors were in East Africa and that these survivors from there repopulated the earth.
It looks like these 'Hobbits' survived the Toba eruption too and aren't part of the East African gene pool of 'modern' humans.(?)
Seems like rising water would kill off the shorties first. ;’)