Why does Microsoft not allow you to link a build configuration to a publish profile. Instead it tells you to use the dropdown in the main VS interface.
By pure luck, I found this:
http://blogs.msdn.com/b/webdev/archive/2012/06/15/visual-studio-2010-web-publish-updates.aspx
If you install this update (related to Azure), then the publishing tools are updated to a wizard type interface that DOES tie a publish profile to a specific build configuration.
I don't really understand why this is tied to Azure, but it works perfectly for all types of publishing (I use the publish to a folder option). No more publishing with the wrong build configuration!