Setup.exe Only Uninstalls the Game?

Ok, so I have been at this for hours with no avail-
I have the legitimate purchased base game on disk and wanted to install the expansions using torrents. I was initially able to install the Into the Future expansion and able to have it show up on the start menu, however I was met with the message that I was not able to play the game due to it being an unauthorized version. I looked up what to do and attempted to update my game and apply the ultimate fix. After doing so I found that the icon for the Future expansion had disappeared from the game launcher. I then tried to reinstall the expansion using the setup.exe application, instead of showing the usual installation wizard, it showed the uninstallation wizard. I have since been looking for a way to fix this without any thing to show, I have re-extracted the torrent files, deleted and attempted to uninstall the expansion (however it still shows up in my programs in the control pannel) replaced the relevant files in the game/bin folder but nothing seems to work. Every time I try to install the expansion, the setup application tries to uninstall it. 

I've looked online and in other threads but I can't find anything that relates to my issue, anyone have any thoughts? 

TL;DR (Expansion) setup.exe does not install game, instead uninstall wizard appears, after finishing uninstall wizard, extension still present in computer programs.