Found a new "feature". With procedures if you copy a XML formatted file with the writeFile command to a client, even if it's a different extension (in my case .config) Kaseya writes a header and footer to the text inside the file! This in my case causes the service that depends on the .config file to error out and not run!
Why would Kaseya think it's ok to modify a file that you're copying!? I don't care if it's XML or not!