I created an FMP12 tool called "Easy Runtime Sign" for myself to make the signing process of runtimes easier. It's uses the terminal script that was originally provided by Christian Schmitz. Please notice that you need the Base Elements Plugin in order to work properly!
How it works:
Just type in your name and your developer ID, choose your runtime and press "CodeSign Runtime". After that you can check the Signature with another button. A detailed description in English and German is also in the file.
Works great for me. Use it and feel free to share.