Have you set the game resolution to match your desktop resolution? I can imagine it gets messed up if the touchscreen uses desktop coordinates while the game window is of a different size.
Other than that, the best I can do is point you to a previous topic:
Wacom Tablet Pointer In Linux? There are no real solutions in there, but a lot of things you can try. I never tested the game with a tablet or touch-screen myself, unfortunately.
GMMan is right though: there almost certainly won't be a fix for this in the official game distribution, so if you want to try to get it to work, you'll have to make do with the options and settings that are in the game now.