I noticed that when I have multiple addon manager's installed according to my program list in the add and remove programs list, I have to uninstall and re-install again, for the buildings to appear, just landed yesterday in Zurich again with no buildings.
The Add/Remove Programs list DOES NOT indicate how many "copies" of a program you have installed. It ONLY reports how many *Uninstallers* you have for it.
Under normal conditions, you won't see two entries for the Addon Manager, you can install it multiple times, and the entry will always be one. But, if you start removing files manually, without using the uninstaller, it's possible the link between the Uninstaller and its registry key will be lost, so a new entry will be created.
Again, this is an entry for JUST the Uninstaller program, it doesn't have anything to do with the actual installation. Having duplicated uninstallers available (the unins*.exe files in your FSX root folder) won't make any difference to the operation of the one installed copy. There's always ONE copy of the Addon Manager running at any time, it's not possible it could "start twice", both because its .DLL file is just one AND because the DLL.XML reference to it only once.
This means the number of Uninstaller entries in the Add/Remove Program doesn't have anything to do with how the program works, or any "missing buildings" problems, if you happen to noticed it and believed it was fixed by removing the double uninstaller entry, it was just a coincidence, what "fixed" your problem was probably just restarting FSX.