It can take a long while for MC to analyse what is already on the phone. MC will keep showing the "Working..." text up near the storage size information in your image until it finishes that analysis. From what I understand, MC can't control what it actually looks at on the phone, relying on Android functions that report everything. Then MC uses that information to work out what to do with the Sync.
Have you left it going for a few minutes before trying to stop it? My Sony phone, which doesn't have a lot on it, would take two minutes or so to finish the "Working..." stage.