Minecarts (all survival varieties) will rotate strangely and occasionally appear to go off track if the track goes up/down or curves. Straight flat tracks are not affected.

From what I can tell, the carts only appear to go off the track (smelter systems still work). They may go off the track into mid-air, onto a block, or inside partial blocks (e.g. stairs–not sure about full blocks).

Relogging does not fix the problem, but the way the carts move does change. Relogging can make carts that were just rotating weirdly before go off the track (in appearance).

I have seen one instance where the minecart repeatedly disappears when it passes a certain spot, then reappears on the rest of the track.