Hi Harry, while I don't have a solution for your issue (other than the suggestion that this might be a problem on the smugmug end), I do have a workflow suggestion.
Instead of choosing “FTP as…”, choose “Upload…”, this will immediately get you into the smugmug uploader (more precisely, the last one used) instead of having to select it each time. You can also use the keyboard shortcut CTRL+CMD+U.
Cheers,
Hayo