I have this update installed but when attempting to install it again I am informed that the file is already installed.
If our installer says you don't have the 9.1 update installed, then you don't have it...
For proof, check the following two files:
Right-click on each, select "Properties", then "Details", you'll see the version number and it will probably be something like 9.0.xxxx, meaning you don't have 9.1 correctly installed.
This might happen if you installed 9.1 over a patched or modifed FS9.EXE or G3D.DLL, so the patcher has not completed.
You can try to restore the original files from inside the .CAB files in the FS9 installation CDs, then you need to remove the BACKUP folder and try to run the update again.
NOTE: having FS9 in a situation like yours, with mixed files coming from 9.0 and 9.1, is even more dangerous for stability than not applying any patch.