Sounds to me like you have several copies of the database... probably 2 or 3..
before you copy any databases you want to make sure they are closed before copying. All databases will show in iTunes unless they are a remote database.
If you were to use "open in" to move the file from a Drop Box folder into the FM GO sand box, you are given the option of adding a second copy of the file by appending a number to the file name or replacing the original with the new copy. That might be a simpler way to go that using iTunes.