You don't have two Addon Manager installed, you have two Addon Manager *uninstallers* registered to the Windows Program list, which means Windows knows there are two ways to remove the *same* Addon Manager, since there's always only one installed, which the bglman.dll file in the FS9\MODULES folder, or the bglmanx.dll file in the FSX folder. It's probably related to the fact the Cloud9 installers used a different installer module than FSDT's (Cloud9 used Installshield, we use Inno Setup)
It's basically just a cosmetic issue of the Windows Add/remove program list, if you don't like to see it, "uninstall" both of them, then reinstall the Stand-Alone Addon Manager, there will be only one entry. However, the Addon Manager you had installed was always one at all times...