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.
Hi, You can drag and drop the project file to Eazfuscator.Net and it will handle the Obfuscation of your binaries every time you compile with release, if you are using different Obfuscator check how to obfuscate the project file, I believe rebuilding your solution is recompiling the .exe and overwrite your Obfuscated .exe then the setup project will include the new non-Obfuscated file.