Hi Mikey
The automatic installation for the Game Launcher does not normally use Program Files Folder but should be in the Program Files (x86) Folder.
If you install the Game Launcher from here
http://forums.ubi.com/showthread.php/675733-Ubisoft-Game-Launcher-Download-Forums
You have the option to install it in any drive and in any folder.
In the Control Panel you will see that it changes from the normally installed Ubisoft to a Uplay Game Launcher.
If manually re-installing uninstall from the Control Panel as a corrupted install will still add parts of it
Delete the Ubisoft Folder in the Program Files Folder.
Run a registry cleaner to remove any remains and reboot the system.
As long as the Silent Hunter 5 game downloads ok.
The Game Launcher can always be sourced at any time from the recognised third party download link shown above (Ubisoft Sweden).
Peter