To quit the program, use the quit button, or quit from the menu. You should not quit the programby killing its window. This causes a harsh death and the cleanup routines will not be executed.
The sync button will sync four the main applications and any plugins that are installed.
This will sync the main applications and any plugins that are installed and then do a backup of all databases and programs. It will only backup changed files, so the first time it will take a while. Subsequent backups will be a lot quicker.
If the backing up encounters an error, maybe your serial speed is too high. Check the FAQ for more info.