Wholesale discount product without an addon upgrade applies proper discount. See Product total line at very bottom. (click to enlarge) 

Wholesale discount product with a single addon upgrade (of $10) applies no discount.  (click to enlarge) 

You can see both products in cart. Bottom product has proper discount applied. Top product with $10 upgrade has discount apparently applied to base product but it is not reflected in the subtotal, even to base product alone. (click to enlarge)