If this is a mac system, enable spotlight. This utility must be enabled and have indexed your hard drive before the updater can find your installed copy of the software.
Yes it is a mac, Mountain Lion. My Spotlight is enabled. if I search for Filemaker Pro it comes right up in spotlight?
If that wasn't the issue, try downloading a new copy of the updater and try again, maybe something got "munged" during the download.
If all else fails, FileMaker Tech support doesn't charge for help with installation issues so you might try calling them.