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
It turned out to be a missing (non-web) DLL in the MSI, which I assume was used by the pages giving the error. A quite misleading error message I'd say, as the page was certainly precompiled, but had a missing reference to that DLL.