I caught this issue when we demoed Communique to you a while back. We've have not had a chance to address it yet; however, it is on the list of to-dos for build 306.
The best way to address this issue is to eliminate the tracking number and sum up the entire costs for the order as a whole (instead of by tracking number). This would make a more accurate comparison of the acutal shipping collected vs. the total shipping costs for the order.
For the vast majority of customers, it's one order and one package, but we do have some like you who have multiple shipments for the same order so this change will benefit all.

Thanks for the feedback,
Delphi Centurion