I'm sorry, but what you said simply cannot happen, normally.
When it happens, it's because some other software you are running, most likely an antivirus, is messing with the installation, blocking some files, and let other passing through and, if you end up with mixed up files from old/new version, this will surely cause problems and crashes.
Haven't you seen how the installer works ? They ALL download the files, and the files are downloaded from the SAME location so, it's not possible that installing a scenery or the Stand-Alone Addon Manager would get you different versions. Again, not possible, if there's no outside interference, like the antivirus problem.
We only had ONE problem, which of course has been fixed in the current Stand-Alone Addon Manager, and it was an error on start from Couatl, saying it couldn't create some objects from XPOI, when you never had XPOI installed. This was discussed on the forum in many threads, and the solution would be removing the XPOI folder which was installed even if it shouldn't. The current version of the Addon Manager will automatically clean up that one, if it finds you didn't had the product installed.
Also everything you did was entirely unnecessary, you only had to download and install the latest Stand-Alone Addon Manager after all the sceneries, and it would have fixed everything.
If you still have issues after doing this, please clearly indicate them, by describing precisely your problem, so we can say if it was a problem of the installers, or a problem of some external interference, like the antivirus or something similar messing with the installation.