I don't know what used to happen in the past, but these days it is a fixed program, and has been for a number of years.
It is a fixed alternating program, riders board and are put through a very tame cycle. After which everyone is asked if they would like to stay on for a more intense cycle, or leave, those that do want to leave are let off, then hose that remain are put through the second cycle.
I don't know any definites, but I think this is done for two reasons:
 - Because the ride was never designed to be used with water, and as such, it now has a drastically reduced lifespan. I believe standardizing the program has been done to make the most of it's remaining life span.
 - An added bonus to point 1, is that the first program will appeal to Chessies target audience of young adventurers, who have only just reached 1.4m, and might think they can cope with the first cycle, but maybe not the second. Plus with a lack of extreme thrills in the park, it's a bonus double ride for older adventurers without queuing.