To fix this problem, do the following:
1. You need a clean and patched up version of RTW.
2. Download all the RS2 files, as shown in the release thread.
3. Now, install the RS2 mod to a new folder, created on the desktop. Mine is named Roma Surrectum 2.
4. When the mod has been completly installed, copy and paste the entire contents of the Roma Surrectum 2 folder, located on your desktop, to your freshly installed RTW game. folder.
5. The new launcher that has been created on the desktop doesn't work. This is because it is a shortcut that the installer has directed towards the Roma Surrectum 2 folder located on your desktop, which isn't a game folder. To fix this, right-click the shortcut and change the Target and Start In lines so that both point to your correct RTW folder.
So in my case, "C:\Users\Al Simmons\Desktop\Roma Surrectum 2\Roma Surrectum II.exe"
becomes "D:\Activision\Rome - Total War\launcher\Roma Surrectum II.exe"
etc.
6. If you did everything correct, the launcher on the desktop works. If it doesn't delete it and create a new shortcut from the "Roma Surrectum II.exe" file located in Activision\Rome - Total War\launcher.
Enjoy!