If you purchased the tickets from an outside vendor, they may not be "worth" what you paid for it. When you upgrade the ticket to an AP, they only use the value disney was paid for the ticket.
Random Example: Disney sells a ticket to "Joe Bob's Ticket Outlet" for $10. Joe Bob's Outlet sells the same ticket for $12. You want to upgrade the ticket to a $50 annual pass - but to Disney, the ticket is only worth $10. Thus, to upgrade, you would owe Disney $40.