There are several things that can cause this situation.
The first is that the original citation payment was made after the maximum 21-day period and therefore increased due to additional penalties. The partial payment of the increased amount would have been received, but the citation would still be referred to DMV for collection because of the balance due. In this case, the total amount is still due to the DMV. It is advisable to pay the total fine amount to DMV so that the vehicle registration wont be delayed, causing additional fees. The original payment can then be refunded if proof of that payment can be provided. To receive a refund of this nature, contact the Parking Supervisor at the Irvine Police Department, 949-724-7037.
The second possibility for this to occur is that an error was made when posting the original payment and it was not credited to the correct citation. If you have proof of payment for a citation that the DMV is showing due on the vehicles registration, contact the Parking Enforcement Center at 1-866-453-3603. They will instruct you on how to provide the proof of payment. They can also issue a letter which can be provided to the DMV once the error has been corrected.