you're doing what you need to do. CS is not predicated on parental rights. It is determined by parental responsibility and is a separate situation. Pay the support for the month and ask the courts if you can get it back when you get in to court.
if any additional monies are paid on the other account, all that would do is make dad ahead in his payments. When all this gets cleared up, he would have a positive balance on his account so I would think he could short the next payment that much and still be up to date but do not take this action without verification from the CS office. They seem to have their own methods of accounting.

