I wonder if at really low speed the RS board is thinking you are starting up and tosses in it's startup chuff. I don't know that I've ever seen that, but maybe I just didn't notice.
You most certainly want to set the chuff by hand, you'll never get it accurate at 1/4 driver rotation running it. Also, I apply light friction with a finger to the flywheel so it doesn't drift back and toss in another tach pulse. Sometimes it takes several times to get an accurate chuff rate.