Did you get a refund for the fare they claim isn't included in PQD? It would seem to me that if you paid the same fare for the ticket and were not issued a refund (compare the fare parts of the before and after change receipts) then the PQD should be based on the fare paid for the ticket - not the fare you would have paid on the date of change. Basically - does UA still have the money? And if so, should you be getting it back?
On that note, if you had a flexible-refundable ticket, are you sure they didn't refund the rest to your form of payment?