I think the problem was that the timing had to be spot on between all three cannons and the two vehicles so that neither the sensors on the cannons or the sensors on the cars registered an incursion and shut something down.
I wonder if removing the middle cannon would help. Allow enough space for both ride vehicles to park and not be as in the way of the cannons as they could be now, give them some "breathing room" as it were. Both cannons are extended as the vehicles enter the scene. The first one fires and retreats, then the last one at the far end. As the vehicles start to roll past the first one, the last one rolls forward again, vehicle stop, it fires and rolls back out of the way.
And if the cannons aren't going to move at all, maybe they could add some oomph to the scene by adding vents in the ceiling that poof out a big but quick blast of air in sync with the firing of the cannons.
-Rob