I am using Magento ver. 22.214.171.124 and shipping_override. However, the problem existed before the addition of shipping_override (and after).
The system gets UPS rates using my UPS account. However, the checkout always shows about 6% LESS on any selected rate. When logged in viewing the shopping cart you can see BOTH amounts.
This has nothing to do with the tax rate, or shipping_override. The flat rates from shipping_override are also reduced and I've tested with no-tax states. There is no added charge setup (either fixed or percentage).
Its a mystery. . .