The problem doesn't have anything to do with any of our products, but is surely caused by the mis-match of files between the 9.0 and 9.1 version. It's not just the .DLLs that change, many BGL files from the default scenery are also patched.
You can try to remove the BACKUP folder, which is a backup the FS9.1 installer does and, if it's present, will prevent the 9.1 install to proceed. Also, be sure you run the FS9.1 setup executable from the FS9 root folder.