I did the upgrade myself a few days ago without issue. Sorry I have nothing more to offer as a solution to your problem. You should make sure your FMPA application is in the proper place on your system drive . . . in the Applications folder.
If this is the same issue that occurred with the 11.0v2 on Mac OS X, then your problem is probably with the Spotlight index being incomplete.
"Make sure Spotlight is enabled and that the indexing has been completed. Apparently, the installer uses a spotlight search to find a valid copy of Filemaker."
If for some reason the spotlight index is done and it still doesnt work, try checking your Spotlight Preferences located under System Preferences. Make sure you check the privacy settings to make sure you don't have something excluded. Many people have had luck with unchecking "Applications" waiting a short while and re-enabling it to force an index update.
If all this still does not work, then lastly you can do the following if you suspect your spotlight index is damaged in some way:
Under OS X, I have run into an issue where the Spotlight index is damaged or non-functional. Open the Terminal application which is located in the following location: /Applications/Utilites/Terminal.app. Then input the following commands:
sudo mdutil -i on /
sudo rm -rf /.Spotlight*
sudo mdutil -E /
Type the above commands exactly as they are shown. Be advised that you will be prompted for an admin password at least for the first time. Once you have issued these commands, Spotlight should begin indexing in a few seconds. Check the Spotlight menu to view the indexing activity. Once it has completed creating it's new indexes, the Updater should work without a problem.
The problem was solved by Filemaker sending me a new application dmg rather than the upgrade.