Mean Repricer may not reprice correctly if you use both Shipping Rate Tables and Shipping Overrides on your Amazon account. 

Shipping rate tables and shipping overrides will work correctly only separately. You can decide which function you would like to keep using and disable the other one.

Then, you need to click the "I have changed my shipping costs" button in Mean Repricer Console section in order for Mean Repricer to recalculate the shipping preferences.