I was having a similar problem in an earlier snapshot with a teleporter I'd built. I had it set up so you had to stand on a pressure plate and hit a button simultaneously in order to trigger the command block, then when returning, sometimes either the button or the pressure plate were stuck in the 'on' position, making the teleporter behave incorrectly. This would only happen when teleporting to a location far enough away that the server would unload the chunk the teleporter was in, but it wouldn't happen every time, maybe about 30% of the time. I haven't had this problem since the 1.4 prerelease, but maybe I've just been lucky.
Ingolf Dalbo
I was having a similar problem in an earlier snapshot with a teleporter I'd built. I had it set up so you had to stand on a pressure plate and hit a button simultaneously in order to trigger the command block, then when returning, sometimes either the button or the pressure plate were stuck in the 'on' position, making the teleporter behave incorrectly. This would only happen when teleporting to a location far enough away that the server would unload the chunk the teleporter was in, but it wouldn't happen every time, maybe about 30% of the time. I haven't had this problem since the 1.4 prerelease, but maybe I've just been lucky.