Hmmm...
For example, did you use the Editable mesh modifier at all?
I don't know why it is there, but it always comes up under 'Morpher' after fixing the model with Mk's script.
If you use that to edit the vertices, it doesn't like to co-operate with other models.
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Maybe you are you trying to morph something into the same thing
Are you trying to morph your original vertex into the clone?
I used the Edible mesh modifier.
Then I copied it, and tried to select it, but it wouldn't show up.
Fixing it didn't do much either. They still won't select each other. :l