The Scooby trains (cars) are paired up for dispatch, lift and unload and lately there have been 16 trains running. 99.9% of the time there are an even number of trains. When dispatched it follows the same rule as all the other blocks (waiting for one to clear before allowing another to enter), it may look as if the rules are being bent a little but the station its self has around 12 separate blocks. The two trains at load will not dispatch until the lapbars on the front and rear train are down (eight in total). As for the delays at each brake set then that is most probably due to station stops as already pointed out. The computer is programmed to eliminate this start/stop problem as the ride starts up after a station stop or indeed a fault needing reset by Tech Services, it holds cars for a couple of seconds to allow the car in front to make some distance, this is called the "stack up delay" and its possible you were in one of the cars which was having the delay(unlucky i guess). This stack up delay comes into effect when cars start to start / stop and is designed to keep the ride flowing smoothly most of the time. If there was a total computer failure then the ride would be 100% safe as each brake set has a Emergency brake which is spring loaded and defaults to closed, even if the air pressure is lost then Emergency brake will close (funny enough the other brakes would open)
Hope this clears a few things up