My guess is that they are afraid of the older hen. At that age she greatly outranks them in the pecking order. Younger chicks in that situation tend to form a separate flock most of the time, avoiding the more mature chickens. So they tend to spend their time in the coop when she is in the run to avoid her.
All that is perfectly normal and really to be expected. You might find them on the roosts when she is on the coop floor if they are locked in the coop together before you let them out in the morning.
Eventually they will mature enough to work out a place in the overall pecking order, including that older hen, and form one flock. That normally comes when they start laying.
One good thing is that they are watching that older hen, learning from her even if they are avoiding her. She will teach them where to lay and how to act like chickens.