Windows Server 2008, IIS 7.5. Using "Web Deployment Projects inside of "Web Setup Projects" to deploy web services. I had some Web Services installed. When I installed a new one and targeted a different app pool, all the existing services were switched to the new app pool after the setup completed. Any ideas as to what might be causing this?
After searching a little bit more, the following question and answer set me on the right track: How can I create a new application pool in a Web Setup Project?
After seeing the above, I perused the codebase of the solution I'm working on for classes that inherit from Installer, and found several. The problem appears to be that in the overriden Install method, they were changing the app pool for all of the virtual directories that belong to the site to which the package is being installed.
In short, what I thought was a setup config issue is really an annoying custom action issue.