Shipping on cart total not calculating on variable products

I use the flat rate shipping on my website and use the shipping classes to calculate based on the product costs. I have it set so when there are multiple classes in the cart, it calculates based on the highest shipping class.

EXAMPLE 1: Item 1 is $100 and charges 7.5% for shipping and Item 2 is $50 and charges 10% for shipping. Since there are 2 classes being used, it would charge 7.5% on the cart total of $150, $11.25.

This works great except when I have a product with variations in the cart. Any variable products added to the cart are not added to the shipping calculation even though they are counted in the subtotal unless I switch it to charge every item by shipping class.

EXAMPLE 2: Item 1 is a simple product that is $100 and charges 7.5% for shipping and Item 2 is a product with variations that is $50 and charges 10% for shipping. The subtotal on the cart is $150, but it only charges shipping on the simple product for $100 at 7.5%, $7.50 instead of just as it was in example 1.

I have tested with multiple product combinations and checked all my settings, it appears to be a glitch, please help!