I am sure Chas will correct me if I am wrong on this, but I believe this cleanup cycle is similar to a "purge" feature found on any tub with multiple pumps.
If you have more than one pump and you didn't use the tub for a period of time, that would mean you would have stagnant water in portions of the plumbing. This can be problematic and lead to moulds and other issues. Therefore most systems incorporate a purge or flush cycle where all pumps and blowers go on high speed for at least a minute to move all of the water through the spa.
I also make it a point to tell people to leave diverters in the neutral position when they exit the spa. The system can only flush the plumbing if the diverters are set correctly. Imagine you went away for a month and water sat in a portion of the plumbing without moving...