Ok I managed to find an FAQ from the developer and this is what was written...
Q. How can I set it to launch my favourite messaging program?
A. It launches the default messaging app. If it doesn't launch the app you want, you have to clear that app from being a default messaging app. To clear an app from being the default, go to Settings -> Applications -> Manage applications -> Messaging -> Clear defaults. It will ask for which app to launch next time.
The strange thing is, I do this, it says that the stock txt app ISN'T my default, says GoSMS IS, yet SMS Unread count still opens the stock app. I have no idea what to try. Could this be a LeeDrOiD problem?