Besides this the entire registry still includes couatl, virtuali and FSDT entries and in the %appdata\roaming path was a folder called virtuali. I deleted all of it!
We don't put anything in these registry entries. The only key should be your Serial Number in the registry, which is obviously not removed when uninstalling, otherwise you'll have to reactivate after uninstalling.
But it's possible Windows itself has set some flags about the executable (for example, to store the fact you trusted a module), but it's all normal.
Files in the %APPDATA% path belongs to GSX or store your custom configuration like key redefinitions and such, so they are obviously not removed (no uninstaller should remove user preferences) but they surely can't cause any problem.
When I started FSX, first a message popped up, that Zurich is still shown in the scenery.cfg, but not available.
Our uninstaller correctly remove the Zurich area from the scenery.cfg. If it hasn't on your system, it further confirms something is very wrong in your system.
Therefore I installed the latest Zurich v2.5.2 again. The behaviour was the same as it was before, no buildings, just jetways and periodically paused FSX ~2/4 sec.
This even more proves your system configuration is wrong, because it simply doesn't happen
But even I installed Zurich from the scratch, my previously entered serial was still recognized. This shows to me, that the deinstall was not successfull.
This not a proof that deinstall wasn't successful, at all. Your Serial Number is obviously NOT removed when uninstalling, and it's made intentionally, so you won't need to reactivate when just uninstalling/reinstalling.
Are you maybe running FSX into "Compatibility mode" ? This is wrong, is not how FSX defaults to, and it creates all sort of problem, like missing objects, files in the wrong folders (as you described it).
Turn every Compatibility mode in the "Compatibility" tab in FSX and reinstall.