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
For me, I had a script that deletes the production folder and then copies up the new files.
The script failed to delete the production folder properly leaving that the old and new files were mixed in together causing the error.
I manually deleted the entire folder and redeployed successfully...then updated the script.