Shipping Problems : Shipping Added To Cart Twice

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Hi, I'm currently using two POD suppliers. One supplier sends customers the tracking info on their order automatically and one does not. One is set to my stores location and a 3rd party location by the other POD supplier. I am having customers add two products to their cart and each product is fullfilled by the separate companies. It is charging my customers shipping twice even know I have the flat rate method selected. Everything was going fine until I added  second POD supplier that their app doesn't manage the shipping. Can anyone help me out so the customer is only charge once?