Regarding what Ben said, in previous versions, there were some issues related to IPN. In the current version, there are no known problems that would cause a problem like this... leaving any such issue to something outside of DT Register.
As Ben said though, if you did have a problem, you can often resubmit the IPN request from PayPal and push it through.
Ben - can you tell me how you were able to manually enter the URL's for the IPN to go through for those records? I have a bunch of registrations that came through this morning, if I could just manage to retrieve those records, perhaps I can start fresh again. Please reply on how I can do this.