There are a few reasons this can occur - in my instance I found that the PrecompiledWeb worked fine if I pointed my local IIS at it, but when I copied it to the live server, some of the pages - and critically, 3 out of 4 of my webservice .asmx pages wouldn't work with the above error.

It turns out the pages which failed referenced a number of DLLs in the GAC which were on my development PC but not the deployment server. In my case it was the Microsoft Enterprise Application Blocks, but this could have been any referenced assembly. I had the Enterprise Library 4.0 registered in the GAC on my PC and referenced by the website, but only version 3.1 on the deployment server.

So, the only nastiness really is that the error message is misleading...