Try to follow the suggestions found in this thread here:http://www.fsdreamteam.com/forum/index.php?topic=1332.0
Basically, if you try to update FS9 to 9.1 with files ( FS9.EXE and all the stock .DLL in the MODULES folder ) that weren't the original versions, the update will fail over those file.
Or, the same would happen if you applied a nocd patch to FS9.EXE that wasn't made for FS9.1 but 9.0 instead.
Both situations are quite dangerous for the sim stability because having a mix of 9.0 and 9.1 is probably worse than not having any update installed.
Another way of fixing your installation, might be deleting FS9.EXE, then deleting all the .DLL files in the MODULES folder (ONLY the ones coming from Microsoft, not any 3rd party module) and then inserting the FS9 CD1 and launch setup to Repair the installation, then updating to 9.1