Problem with my Pokemon

[RisinDevil]

Last night I loaded my save file to put some more pokemon on my team and I noticed I had some pokemon twice but I didnt think anything of it because I would make whole new teams even if some of the pokemon were the exact same from a different team so i deleted all but one of the exact pokemon. I go to edit my Pokemon again, now that I know I had no exact same pokemon, and I some of my pokemon had been changed into different pokemon that are the exact same but it wasn't that way last night I don't know what caused this. If it helps any usually I throw in a pkm file onto a box slot and then edit as needed (because I downloaded Kazo's Smogon database thing) Wondering if there was a way to do this so that it doesnt mess up? Do I have to drag the pkm file to the editing box then set it in the pokemon storage box? I really like the UI of PokeGen over PokeSav and I don't want to have to use PokeSav to make my Pokemon (though may use it to give the pokemon my Trainer name and ID though since they have a button for that)

[Codr]

You need to provide a more clear example, with detail, of what you're doing to produce this problem. If you can't even reproduce it yourself, it's possibly not going to be easy for me to do so.

[RisinDevil]

Okay, I was making pokemon teams and the way I would do it was by dragging .pkm files into the Storage Boxes (which also didn't update in number till I edited and set one) and then saved when I was done. In the latest instance I opened my file and one of my Nidokings was cloned next to itself over an existing pokemon which is what the program seemed to think was saved that way because it was like that when I loaded up my game on the DS.

[Codr]

Are you even using the latest version?