John - There is no CopyIconFiles step, just “CopyFiles”, so that must be something that you modified. If you’re copying your appname.icns file, where are you copying it to? It should have the Resources Folder set as its destination.
If that’s correct, have you defined the project’s “File Types” under the OS X build’s specific Inspector?
Hmmm… It’s evidently a script based on “Copy Files”. Maybe it’s something that looked useful one day and turns out to be not so helpful. I sure don’t remember making it myself, but then again there’s a lot I can’t remember these days…
The one thing I did that seemed to make a difference was clearing out my old MacType settings and replacing them with “???”. It looks like doing that suddenly let all of the other icon settings (UTI’s, icons, etc.) take effect.
A reboot also got everything applied to all of my existing document files.