Come to think of it, yours is probably the first instance of a Pakistani applicant being rejected on the grounds of PCC. There were reported refusals for Indian applicants for the same reason in Sep/Oct which led to this whole debate on time-bound and geography-bound PCCs and getting it from federal passport authorities instead of provincial police authorities. Pakistan doesn't appear to have such a system - the CIC page appears to imply that city-based police authorities are fully authorized to issue PCCs after you provide them with the NIC which, presumably, might trigger a search on some central database maintaining criminal records of all citizens across the country. Hope you get an early resolution to this and have a successful application this time around.
All the best!