It's quite difficult to help you without having any details about your configuration.
It's been a while since I last tried that installer so, I downloaded, and after the security prompt, it's supposed to either proceed with the installation, or ask you to browse for the simulator, in case it's not found.
Since I don't have FS9 installed anymore, I got the prompt to browse for the simulator folder, since it couldn't be found in the registry. At that point, I exit the installed, since I'm not going to reinstall FS9, considering we stopped supporting it in 2011, which is 7 years ago...I don't even have an optical drive in any of my system so, I couldn't reinstall my old FS9 disk even if I wanted.
This means, I can only guess.
Maybe, there might some kind of problem with the FS9 registry key, so the installer found it, but was somehow wrong/corrupted/pointing to the wrong folder ?