This package was difficult to package, but I finally worked out the details for deploying an Enterprise licensed package.
First:Use Universal Unpacker to unpack the executable into a sub directory. Next, create a folder with the newly-created sub directory, the license.properties and the standalone.properties files, and a batch file, which does:
1) creates a %TEMP%\installprops folder
2) Copies the 'standalone.properties' file to the installprops folder.
3) Creates the %ALLUSERSPROFILE%\Application Data\Adobe\Flex folder.
4) Copies the 'license.properties' file to the newly-created folder from the previous step. This is where Flex looks for its licensing.
5) Runs the "Flexbuilder_Standalone.exe -i silent" from the subfolder tree that was created in step 1. In my case, it was FB3_WWEJ\Windows folder.
Be SURE to have enough disk space to install - but I can't find how much is enough!
To uninstall silently, use the same -i silent switch