If you installed the Addon Manager, there wasn't any need to update GSX by redownloading it again, because the Addon Manager already did all that was needed. If the message said to download the Addon Manager, it's because it IS the most efficent way to upgrade so, why assuming there has been a "problem" to begin with ?
You don't see the Addon Manager in the Windows Programs list because, since it's not a Windows program, but an FSX addon module, why cluttering the Window program group with something that you can't launch yourself, but needs to be launched by FSX ?
And of course, if you launch FSX, the Addon Manager is there as it always has been and as any other FSX addon module is: under the "Addons" menu.