Hi Bevan,
The behavior you are requesting is not an issue with the module, it is a feature which is not currently supported.
The Cart Manual specifically states the following on Pg.46 in the description of the "Combine Shipping and Handling" feature:
"Combining shipping and handling as a single line item allows you to set a fixed price for shipping by choosing free shipping above and entering a handling charge."
There are many other Shipping Methods which support the Combine Shipping and Handling option however the Shipping Calculator is not one of them.
The available Shipping Methods you can use with the Combine Shipping and Handling feature are the following:
- Zone Shipping By Quantity
- Zone Shipping By Weight
- Shipping By Order Amount
- Shipping By Weight
- Product Level Shipping Costs
- Free Shipping
Hope this helps!