We recently setup a new site on our IIS 6 server which does not download the published ClickOnce application; however, it does upload the actual files to the server in the proper directory.
If I stop the new site and start the old site, it all works.
After looking through all the options, I have been unable to locate the setting that is causing this problem.
Once promising option is the Anonymous access. However, I wasn't able to find the switch in IIS for it.
When you publish to a remote server that has "Anonymous Access" turned off, you will receive the following warning: