This is a complaint that I hear all the time in my practice. Unfortunately, this is a case where the system is just unfair. The idea/policy does make sense. The Court wants to make sure that the child is supported until the order terminates. If there is additional money due to a modification, the overpayment can be kept to cover any future non-payments or reduced payments.
For example: Father filed to modify a support order and the order is reduced by $500. He filed the petition six months ago, so he has now overpaid by $3000. The child support clearinghouse will first look to see if there is any back support still owed. Here Father owes $1000 in back support (arrears). The overpayment will first be used to pay that back support. Now there is $2000 left in overpayment.
The clearinghouse can hold onto that money until the child reaches 18 if the money has not been distributed. If the money has been sent to the other party, you still cannot get the money back until the order terminates at 18 or graduation from high school. This protects the parent receiving support since he/she does not know what the court will decide on the modification. The Court would not want that parent to then have to pay the paying parent back out of child support, nor would it want to risk depriving the child of support in order to pay the paying parent back.