Not really. Obvious stuff to look at I suppose:
a. is your merge automated? Could it actually be executing twice? (e.g.
when you test with a handful, are you doing it manually?)
b. what is sending the messages? Can you
 - disable sending for the duration of the merge and see what is being put
in the Outbox?
 - or maybe find out from the recipients whether their pair of messages is
being sent at the same time or one rather after the other
c. any obvious diference between your test addresses and the real
addresses?
d. if you increase the number of test recipients do you ever see the
messages doubling up?