As I (vaguely) understand it, there are several sensors along the track that "count" the number of cars that pass alongside them using optical sensors. (On most wooden coasters, these are the green blocks you see in the middle of the track .) Fins beneath the car--I presume they're the brake fins--break the light beam between both sides of the sensor, allowing the ride's computers to tell when a full train has passed. In Maverick's case, the sensors would presumably count to three to make sure that other trains weren't being launched into an occupied block. I'd believe it when they say those lights messed with the sensor--as I remember, there were also some strobes, so I'd bet they caused some miscounting now and again.
But, it also begs the question: can't they just move the lights or something? They were bright, but it seems like something could be done so they don't interfere with the sensor(s), even if it means putting a physical barrier between the lights and the sensor(s). But this is Cedar Fair we're talking about, so just shutting them off is the best solution we'll probably get.
This is all based off guesstimations I've made combined with an experience while waiting in line for Raven last year, so I may be wrong. As the ride op explained, the sensors were miscounting the cars, so the computer only read that there were five cars on the train. The computer would then assume that the sixth car was still waiting in the station and send the ride into a two-train mode, in which it would slow the lift chain considerably and then bring the train to a complete stop on the brake run as it waited for that last, nonexistent car to leave the station. Maintenance had to repeatedly come out and reset the computer system... Turns out even computers have trouble counting to six. It turned a 15 minute wait into a 45 minute one, but it was educational, so I guess that evens it out?