Nice thanks for sharing your answer. I didn't figure that one out yet, though I had wondered if you could sort the modules similar to the way you can the menu. The menu I sorted directly in the data, however, through another discussion here.
Ok, I found the answer... I just later realized it was related with sorting the Panel elements:) Anyway, I put my config like this: $Configuration['Modules']['Vanilla']['Panel'] = array('NewDiscussionModule', 'SignedInModule', 'GuestModule', 'MessageModule', 'Ads');