Nothing like this can be caused by installing the Nav Cycle, unless this one installs something that affects your EXE.XML or DLL.XML, which seems unlikely.
You probably still have something not updated or, you installed an older version of the sceneries after KLAS. Download and install the Stand-Alone Addon Manager, that will update any scenery to the current version.
Also, check you see both the "Addon Manager" AND the "Couatl Powered plugin" menus under the Addons menu.