It is DCAA's opinion that the prime is responsible for auditing the subcontractors. See FAR 52.216-7(d)(5), "The prime contractor is responsible for settling subcontractor amounts and rates included in the completion invoice or voucher and providing status of subcontractor audits to the contracting officer upon request." But you're probably not going to allow the prime to audit your books and the prime is highly unlikely to have the auditing staff to audit your FPRP. DCAA is reluctant to audit your rates because the government does not have any privity of contract with you. So what's a subcontractor to do? The prime contractor would have to send its CACO/DACO/whatever a request to have your indirect rates audited. The CACO/DACO would then forward that request to your CACO/DACO who would then send it to your cognizant DCAA office. (Don't you just love the chain of command?)
Is your overall accounting system, which includes the accounting and billing subsystems approved? I'd imagine so with a CPFF subcontract vehicle. What about the prime's overall accounting system (and subsystems)? Part of DCAA billing system audit program is to verify that the correct indirect rates are used and that primes monitor the adequacy of the subcontractor's accounting and billing systems.
Did your company have any adjustments to the rates after the end of last year? Did you process any retroactive rate adjustments for the end of year rates?
A CPFF subcontract type comes with lots of headaches for the prime. I'm surprised that they issued a cost-type subcontract in the first place.