I have this same issue. Unfortunately, changing themes is not an option for me because it is a live ecommerce site using the clothingstore theme.
I have tries removing and reinstalling the plugin. I have gone through the company setting and event setting.
The attendee is only charged once through paypal, but they are registered twice and emailed twice. Also, the redirect page shows that they paid twice and have a negative balance (overpaid)
http://www.thewhitepeacock.net/registration
Any other information that I should supply?