Minecarts with command blocks are completely unable to run in the first 3 ticks that they have existed for. They only process their command on the 4th tick even if they are powered the entire time. However, if a command block minecart has already existed for at least three ticks, it is still able to run on the first tick that it is powered with an activator rail. This can be easily seen with the new /tick commands, freezing the game and then stepping each tick to view that a command block minecart can only possibly activate on the fourth tick since it has existed.