credit card auth. vs. charge etc etc

OK, I am looking  for ideas here.  We offer free shipping on most orders over a certain dollar amount.  The key is that it is most orders.  Netsuite does not currently allow full control over this (i.e. we cannot exclude items or price levels).  So we have to allow the shipping to be calculated then go back and remove the charge on qualifying orders. 
While this does cause confusion for the customer, most are appreciative enough of the free shipping to not complain (gift horse....mouth..yada-yada).
The biggest problem this causes is in credit card processing.  The authorization is for one amount, then the shipping is removed and the actual charge is lower.  Even though it is lower, it still does not apply to the original authorization which results in "double charge" to the customers card.