Any shipping module that uses weight for the calculations also takes into account a built-in Tare weight. The admin configurable Tare adds extra weight to compensate for packaging materials.
To change the Tare point your cursor at the Configuration menu, choose Shipping/Packaging from the menu and change the Tare.
You can set either and/or both a percentage or weight for Tare and Large Package.
Entered as percentage:weight
Examples:
10% + 1lb = 10:1
0% +3lb = 0:3
5% + 0lbs = 5:0
This way both the Tare for small to medium packages has a flexible option of percentage + weight and the Large Package increase has an option of a percentage + weight.

