That doesn't have anything to do with our sceneries or our installers, something else coming from another product has changed a parameter in your EXE.XML file, to set an option that enables manual loading for all modules.
Open the EXE.XML file, located at %APPDATA%\Microsoft\FSX and check the following lines:
<Launch.ManualLoad>False</Launch.ManualLoad>
This should be set to False, we don't touch that setting at all, assuming that you (or another product) might have a reason to set it to True, for example being able to manually check what's being started.