Hi Zak,
I too am getting the error message "Some files on the server may be missing or incorrect......" since upgrading Muse to the latest version. The site has been working fine previously, how do I find where the issue is?
I did notice that on export, muse changed some file names that had brackets. I have since changed these file names, and any references I can find to them, back to have brackets but I am still getting the problem.