Somehow between last night and tonight my decks rearranged themselves (maybe because I upgraded from 3.1.2 to 3.1.3?), I searched through the manual and tried various dragging while holding down key modifiers but couldn't get them to rearrange.
I thought to look at the composition setting file and thankfully it is just XML and even better the wrong deck order was reflected in the settings file. So a couple of copy and pastes later I had the order corrected and this was confirmed when I relaunched Avenue.
Update: The next time I launched Avenue the decks were all rearranged again.