File associations and ClickOnce Application Reference files

[C# Programming]

When I publish my C# application using Visual Studio Express, and install it, it creates a ClickOnce Application Reference file on the desktop and in the Start Menu instead of just a normal .EXE file - and this is screwing up my File Associations. Could someone kindly suggest how I could have txt files etc opened in my application when dealing with Application Reference files?

Thank you