Just an update in case someone else has this issue, Nicole from Admin pointed out to me that I needed to re-apply my shipping profiles to my items.
After USPS increased rates I changed my shipping profiles and most recently I created new flat rate shipping profiles, however, I didn't reapply my profiles to the items. I was not aware that this had to be done each time. So, hopefully this clears up the issue, I will have to wait for another similar transaction to take place to see if this resolves the problem and will keep you posted.
Thanks Camilla & Nicole for your help!