Does using the registry disturb the use of settings?

I'm using clickonce. I have managed to create the file association in the Publish Options window (through the Publish tab on the project properties in VB 2010 Express). I have also managed to create the file association by adding a file association tag in the app.manifest. Both work as far as getting the icon to appear for the associated files and also getting my application to start when doubleclicking them. However I can't get Windows to pass the filename argument in the CommandLineArgs without the CreateSubKey code block. Is there a way to get Windows to pass the filename argument without using the registry? Is there some detail in the file association method that I'm missing?