I'm using the lastest version and just tested, the money was correctly deducted from 13600 to 10600. As soon as you confirm the treatment and after the game loads to the screen where Aya is on the operationg table, the money was already lower by 3000. Maybe it is a bug from the saves you're using? I'll link a test save with Aya pregnant. Check the money on the menu and then select treatment. Oh and Ryon only really talks about the value the 1st time you meet him.
The game logic that handles this is located in: "HotB/story/a10/cure_Yes.gml". I'll attach this file, so open it with a text editor and compare it to yours, see the two instances of the value 3000, first the game check wheter or not you have 3000 or more. If you do, a few lines bellow, the game subtracts the 3000. This file is a game logic file and is not affected by the translation patches, so your bug must have been caused by something else.
Also, if you want you can alter this value to fit your purposes, just be careful to not alter other lines or you'll break things. Another simple solution you can do is to edit your savefiles and change the value in line 32, that is your amount of money. Each save has 4 parts, but you only need to do this on the first.