I have an ASP.NET MVC 2 application.
I had this same problem today. I published my web project and realized that not all of the reference DLL's were there. In particular, the indirect DLL references.
It turns out that the directory in which I was publishing to was out of disk space (network share). I had just enough space to publish all the files except for few indirect reference DLL's. The sad part is that VS08 didn't throw any errors. It just published the files are usual. I cleared out some HDD space and everything worked fine.
I didn't find the HDD space issue until I tried to manually move the DLL's over.