I suspect, from this question, that you are manually obfuscating the file. When your setup is built, though, it rebuilds the executable, so that the file is no longer obfuscated - (you'll see the same behaviour if you manually apply a certificate to your code). The trick is to run the obfuscation process as a PostBuild process - which means that the setup will get the obfuscated version.
I was brought up to respect my elders. I don't respect many people nowadays.