Please correct me if I'm wrong-
When upgrading tickets, you pay the difference between the GATE PRICE of the ticket you have, and the GATE PRICE of the ticket you want. Your wholesale price or discount does NOT enter into it.
For example, let's say you're upgrading a 5 day, park hopper, expiring ticket to a 6 day, park hopper, expiring ticket (you're just adding one day). The gate price for the 5 day ticket (including tax) is $211.94. The gate price for the 6 day ticket is $215.13. So, the cost to upgrade the ticket is $215.13 - $211.94 = $3.19. it doesn't matter whether you paid the full $211.94, or $202, or $50 on eBay- you will always pay $3.19 for the upgrade at the gate.
If you think about it, how would Disney ever how how much you actually paid for your ticket? Whether you bought them at the gate, or from a discount company, or from your Uncle Bob, there's no way Disney can track down every single ticket transaction!