Handling fee does not work freeshipping with zone rate

I use zone rates for most products except magazine subscription which are shipped free. Based on Ajeh's help in this forum I have a mod in zone shipping module to add handling fee as a percentage of total cost. The handling fee should apply to both free shipping and zonal rate. Everything works well when a customer buys a product with free shipping and a product with normal shipping. However when a customer buys only freeshipping product the code does not go into the zonal rate module and no handling fee is charged. Is there a way to force the freeshipping module to enter zone shipping module for adding handling fee? Thanks for any guidance.
Version 1.3.9f

It occurs to me that if I make the weight of freeshipping nonzero and give a discount equal to the shipping cost it might work. Does that make sense?

Update on this problem. I was able to solve the problem by assigning a fictitious weight and using a built in blank coupon to offset the shipping cost. This way the handling charge is correctly calculated and the customer gets back the shipping cost via discount.:smile: