I'm having some problems as well, although the majority is working.
1) When I change the status on an order, it emails the customer. However, unlike when they first did their checkout, the link to their invoice in that email is incomplete. Instead of DOMAIN/catalog/orderblbablabla it only gives /catalog/orderblbablabla.
Been looking for awhile but can't find where to edit this so it will display the full url.
2) I realize you mentioned that you havent completed the 'Print Invoice' yet, but when I click the button it opens and empty popup (not even doing the stock osC printout.