I have a VS 2005 web site that I publish using \"Publish Web Site\", and I clear all the three checkboxes. I also have a deployment project that picks up the published files
I had the same problem today. Some forums tell about there is are missing reference in your website and it certainly does in your case. Despite you have all the necessary assemblies included, you might been deploying your website in a IIS server with 3.5 framework, right?
Well it was my case, so I copied the web.config file from an original ASPX 3.5 website and modified some parts (removed other 3.5 assembly references) and try deploy it again.