ok, I try to clarify.
The store is on 1.3.9h

When there is a discount on an order, in this case a discount coupon for free shipping, and you change order status to, lets say "delivered", the order total is totally messed up.
Total isnt correct anymore.

See below:

First order is good:

Subtotal: 139:-
Discount Coupon: Test : -69:-
Shipping: 0:-
Tax 25%: 28:-
Total: 139:-

Then changing order status:

Subtotal: 111:-
Discount Coupon: Test: -69:-
Shipping: 0:-
Tax 25%: 11:-
Total: 53:-

This is tested on several stores with same result. All running 1.3.9h.
If removing the Edit Orders module it works fine to change status on an order without messing up the total. But removing it aint no solution since we need this module and its good in all other aspects.
/Jagge