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Ok, here is what I would do. Do you have units networked? If so unplug the network cable on one unit. Go threw the waypoints and delete the doubles. Insert a SD card and save the waypoints to the card. Delete all waypoints from other graph (if you have one). Write down your sonar settings if you need to and do a hard reset on the unit(s).
Insert the SD card back into the graph and import. If you have a network plug in the cable and turn on the other graph. The waypoints will automatically transfer into it.
X2. I have three units networked together and was fighting the duplicate waypoint demon for a while. I ended up cleaning up one unit and then saving my data to an SD card. I then deleted all waypoints, trails, and routes on all three units. Reloaded the data to one unit and then let the other two sync up. I have been good since.
If you don’t have multiple units networked together, I have no idea what would cause that problem.