Incorrect shipping cost at checkout

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Good afternoon. I was just about to make a BFCM discount for my site and advertise it. After making the discount, I went to check it out. The 20% code worked for the products as expected but I wanted to check it out with the shipping. I click to verify (3 items in cart) and I noticed that the price is incorrect.

I have 3 items in the first cart, 2 using the same custom flat rate shipping profile I used and the other on another profile. Shopify calculated one item from each profile and completely ignored the third, totaling $12.50. To further test, I go back into my store and add 3 more items. Now there’s 5 items in the cart and I go to checkout. 3 items from one profile and 2 from the other. It still totals $12.50, ignoring 3 of the items in the checkout for shipping costs. 

how can I alleviate this problem?