Symptoms
Products with "Is Free Shipping" set to yes still add to non-free shipping costs when using a free shipping threshold, and FreeShippingAllowsRateSelection is set to true.
Cause
Free-ship products only get free shipping when the customer chooses the shipping method specified in the ShippingMethodIDIfFreeShippingIsOn AppConfig. The non-free rates displayed when FreeShippingAllowsRateSelection is set to true will charge shipping for all items.