You have two separate issues:
- The double entry for the Addon Manager can only be caused by a problem with your DLL.XML, because the installer surely removes the previous version when installing the new one, but if the DLL.XML had a problem, it might not work.
- The problem of missing buildings was caused by a problem with the new Live Updater, that in some cases didn't update *all* required files. The fix is online now, so you should download and install the Stand-Alone Addon Manager to get the new updater, and this should fix everything, provided you haven't removed anything manually from the Addon Manager folder.