What happens should be exactly the opposite of what you are describing because that is what will probably happen if you manage to fool the installer in some what to install without the 9.1 patch, and try to run the scenery with 9.0 instead. It will probably crash as soon as it starts. That's why the installer checks if you have the 9.1 update installed, in order to not let install something that will crash when used.
So, something must have gone wrong, or you are trying to mix-match the 9.1 with 9.0, which is also another thing that might lead to crash. For example, if you use a nocd crack with a 9.0 exe with the other files from 9.1, it will probably crash as well.
So, you need to be sure ALL your files are the 9.1 version, BOTH the DLLs in the MODULES folder AND the FS9.EXE. If something is still from 9.0, flight sim will have problems. You can check the version of the files by right clicking on each one, select "Properties" and select "Details".