I have an ASP.NET MVC 2 application.
I am having this same problem (different assemblies though). If I reference the assemblies in my web project, then they will get included in the publish output, but they should be included anyway because they are indirect dependencies:
Web Project ---> Assembly A ---> Assembly B
On build, assemblies A and B are outputed to the \bin folder. On publish, only assembly A is outputed to the publish folder.
I have tried changing the publish settings to include all files in the web project, but then I have files in my publish output that shouldn't be deployed.
This seems like a bug to me.