Sometime when I logoff from the game and re-login the game, boat that existing in the world didn't located in a correct position, it flow in middle of air, I have to ride the boat in order to make it fall back to water
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You are not the only one i'am experiencing this as well its been something in 1.4 (it happened in all 1.4 snapshots). Also note that the boats slowly rise then rapidly fall then it starts all over again.
I have also seen a boat that had sunken to the bottom of a 1 or 2 block deep river. When I entered the boat, it rose back to the surface (I was under water for a second or two).
The boats have been bopping up and down and splashing on the surface before 1.4 (at least in SMP), but after 1.4 they have also started to levitate or sink every now and then.
I would like to reiterate that I have been having this same problem as well. Mostly the floating boat, but sometimes the sinking part as well.
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I've had this issue too while playing vanilla server. When I walk up closer to it, it seems to drop back down. I haven't confirmed it has to do with login, relogin, but it seems to happen after I've left boats lying around someplace... sometimes they fall into water too and float back up.
The problem persists in 1.4.4. I didn't relogged, only was distant.
Oh, and they not only fly, but "sink" too...
yeah i was in survival and my boat was just floating up in the air!
I wonder if this is related to MC-119 since mobs and boats are both entities.
Having this problem in the current release version of minecraft. It seems to happen when the boat is sitting near a rapid caused by taking water from an ocean with a bucket (which in itself is probably a bug) but not near enough for the boat to be caught by the rapid. I placed several boats in this area and others and the only ones that rose into the air were the ones I placed about a block away from a square of rapids that are moving away from the boat. The boat is in the square diagonally behind and bellow the rapids and may be pointing away from them. So like this:
~~~~~Rapids ==>
Boat
-------
LAND –
Never mind, found a boat floating on plain water blocks.
It still is a problem in 1.5.1
Eric Goulet, you do have a point about it relating to MC-119.
Boats can also do this if the boat is next to or in a wall of some sort upon a reload of the world. That's where I see it the most.
Correct me if I'm wrong, but I think what happens is that upon reload, the "block" it is in takes the boat as in an invalid spot, so it moves it up a block, thus a "floating" boat.

Is this still a concern in the current Minecraft version? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.