If you have RTW and BI, you should have installed the 1.6 patch and not the 1.5 patch. The 1.6 patch upgrades both RTW and BI, whereas 1.5 just updates RTW. It's possible the installer is now a bit confused as it isn't updating a 1.3 edition of the game. I don't know if there's any kind of trick you can do to resolve the problem other than uninstalling the game and reinstalling it again, this time patching in the game in the correct order. Of course, if you had RTW first and patched it to 1.5, then bought a copy of BI and tried installing it, that might also bring up the problem. So unless anyone says otherwise, I'd uninstall the game, reinstall RTW, then BI, then patch to 1.6. I also can't remember if you need to install the 1.2 patch before installing BI.
You might also want to try the official support forums, the link available on the official Totalwar.com website.
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