We are not as big as you, but we do have one event that we are currently having people sign up for that will potentially have 1000 registrants. I put in the instructions that you may receive more than one confirmation e-mail and that was normal. I have received only one query.
The only way I can explain why some are duplicated and not others is that it is how the code handles the data. Code problems are fixable. It is a matter of how difficult it is.