PAYE Refund Claim

My client, a construction company, has suffered a tax deduction under CIS regualtions which is in excess of CIS tax he has deducted from his subcontractors and staff tax / ni deductions, but HMRC are refusing to refund the difference, despite the client having evidence of the credit he is due. They state this can only be dealt with upon filing of annual returns (P35 etc.). This has an obvious effect on cashflow. Does anyone have any experience of this issue or more importantly perhaps, a process to change the view of HMRC?