Hi Jody,
The option in the OE Company Profile to 'discount misc charges' has to do with order discounts as defined on the Totals tab of an order, not the 'Early payment discount' as what comes from Terms.
There currently are no settings to calculate the Terms Discount Base with misc charges or without. Only tax can be included or excluded with the terms discount base at this time.
_________________________
Regards,
Softrak Tech Support