If I am understanding you correctly, you have different Auction profiles for each weight. A 1 lb profile, A 2 lb profile, etc and a profile for Flat Rate shipping??? You can most certainly do that if you want. That is how my daughter in law does hers. And it works very well for her.
You need to check to see what default email template you have selected for each Auction profile as far as the Shipping notice.
On the menu, go to " File | Auction Profiles......
Select each Auction profile one at a time. Check to see which email template is selected for the Shipping notice. And record the email template name.
Go to an Invoice and open the Shipping notice in an Invoice and see what the text is. If only one line appears, then perhaps when you edited the email template you forgot to save the work. As the notices you emailed me the other day looked fine. So either you have changed something and didn't save your work. Or you have not selected the correct email template for your Auction profile.
You might try sending me one of each of the shipping notices again and so I can see how they look from my side.