The question is, how are you getting duplicates? At buy-in or tournament setup are you entering new players that are already in the database? Doesn't the software warn you that there is already a player with the same name? Or are you entering different names for the same people that are already in the database? Are you importing players from a file? The software should also warn you at that time that the players have the same names as players already in your database.
Because now I have multiple players in the standings listed twice AND they are already listed as being merged.
What do you mean "they are already listed as being merged"?
There are a couple of methods for eliminating duplicate players, but it will depend on what information in the database is important to you. The player database serves 3 purposes, mainly: (1) as a place to store player personal information (address, phone, email, etc; items beyond their name); (2) as a way to uniquely identify players and collate them across saved tournaments; and (3) as a means to divide players into leagues and divide tournaments into seasons.
If you don't mind losing that personal player information, you can easily (well, sort of easily) rebuild a database by deleting all of the players in the database and loading each of your saved tournaments and adding the players to the database or merging them with existing players.
Magic_fubu's answer is a really succinct way of putting it, and is what I would recommend. To give a concrete example, let's say you have 3 players in your database named "Joe", but they all represent the same player, so you need to eliminate two of them as duplicates.
(1) Pick the "best" Joe in the database. That is, pick the one with the most up-to-date personal information. If it doesn't matter, then pick one at random. Delete the other two.
(2) Load your first tournament. Go to the Players tab. See the players listed
italics? Those were players you deleted from the database. That is, those were "attached" to the wrong database player. Press the
Merge Players button (or, on version 3, press the
Database button and then press
Merge players in your current tournament...).
(3) This allows you to match each
italicized player with the corresponding player in the database.
(4) Save the tournament. Repeat with all saved tournaments.
Instead of doing this one player at a time, in step 1 delete ALL of your duplicate players, leaving only one of each player in the player database. In step 2, merge ALL
italicized players.
Once you've made one pass through all of your saved tournaments, you should be done. Make a backup.