I have an ASP.NET MVC 2 application.
I had the same problem with VS2010 and a WCF Service Application.
It turns out that if your (directly or indirectly) referenced DLL's are deployed to GAC, the VS publishing feature excludes them. Once I removed the assemblies from GAC, publishing feature started working as expected.
I guess VS is assuming that if your assemblies can be located in GAC on the machine you build, they will be located in GAC on the target machine as well. At least in my case this assumption is false.