It does amaze me how most of the general public and media don't seem to realise that rollercoasters are gravity powered and once they get moving, there is no control to stop them mid track!
I think Pokemaniac's comments on page 7 of this topic best sum up the most plausible explanation so far. The computer system only has an artificial knowledge of where the trains are based on detecting movement on sensors at the start and end block segments. A computer can recognise that a train has entered a block and will mark that block as occupied until it detects a train leaving - they likely have no way of telling where abouts in the block the train actually is.
If a reboot was to happen with a train stalled, it is likely the blocks mid track would be marked as clear and the system relying on the operators to be aware of any mishap and ensuring the track is clear before starting the ride. Engineering would have been present in the control booth, given the breakdown that was occurring, so it is highly likely that someone with the skills and authorisation to reboot or manually control the ride were present.
As for the empty car stalling in the first place, sending empty trains after a breakdown is very common, especially mid afternoon when the ride is probably running at optimum temperatures. I believe all other stall events on Smiler have happened first thing in the morning? Its impractical to load and unload water dummies for every minor breakdown the ride has. However, yesterday was very windy and you only had to look at the umbrellas around Oblivion on the TV shots to see just how bad it was. I suspect this just added to the bad luck Alton was having yesterday afternoon!
To me it seems like a combined failure of human error and a limitations of the computers knowledge, causing the holes of the swiss cheese to line up and an accident to occur.
As always with an accident like this the focus of the investigation will be how to prevent it happening again. If the above theory turns out to be correct, I suspect we can see an overhaul behind the scenes of computers systems and sensors, perhaps with some new technology so computers can always keep track of a car no matter where it is in a circuit, but otherwise no major changes visible to the outside public and we'll see the ride re-open as soon as Alton can.