I'm assuming this is new because a search brought up nothing. I am now playing an Elf female on the Charlatan's Protege background and have found that if I travel from the train station outside the University to any of the other locations: Boil, Docks, etc. You get 5 coins added to your coins rather than being charged 5 coins.
In Madame Lil's quest, the guy in front of the inn will give you 400 gold everytime you talk to him, before you deliver the cash to Lil.
Heres my guess you took advantage of the flaw in the quest and got yourself some easy cash, then you installed the patch and finished the game. But you didn't try and get cash after installing the patch.