If you are using Super Orders or Edit Orders and an order total discount other than Group Discounts (e.g. Better Together, Quantity Discounts, Military Discounts, Newsletter Discounts, Combination Discounts, Big Spender, Big Chooser, Frequency Discounts, or any other contribution written by someone other than me), the process of editing an order using either of those mods will flip the sign on a discount causing it to appear to be a surcharge.
The fix is straightforward; both admin/edit_orders.php and admin/super_edit.php simply list discount classes ("ot_coupon", etc.) You simply have to add any additional classes you are using to if statements in those two files which enumerate through the order total discount classes. Searching for "ot_coupon" will show you what to change.
The full fix and more notes are on my blog at http://thecartblog.com/2009/12/21/ze...counting-mods/