Zak, can you please clarify which elements of a Muse site will generate the popup alert box, "Some files on the server may be missing or incorrect."
You say:
...Muse only verifies the version and existence of JavaScript files and the page-specific .css file. Images, assets and the global and master page css are not verified.
Does this mean that the only trigger for the error message would be if one or more .js or .css files did not get uploaded to the web host? If any images or assets did not get uploaded, then the error message would not appear?