There is a bug in bukkit since 1.5 which breaks these commands. It no longer tells my plugin when a player exits a vehicle (minecart, boat etc.) so my plugin doesn't remove them.
I made a bug report about this last Friday but it hasn't been resolved yet, until bukkit fixes it the commands are unavailable.
I removed permissions for the minecart and the boat commands, probably made a typo if you're still able to use it xd. I'll properly remove permissions tomorrow, they will be re-added when bukkit fixes it