I've not found a way to resolve it yet, but I have added each of my inboxes to my favorites area, and I can reorder those however I like...
I also have sub-folders that change each semester for courses I'm teaching at that time, so I add those to favorites to get to them quickly. Adding them to favorites, combined with automatic routing rules has made my life so much easier. Now, my favorites bar will show me immediately when I have an email from a student in that course. (Granted, this doesn't work if the student does not adhere to the subject line indicator on which the rule is based, but that's rare, and even if they do, it still shows up as an unread in the general mailbox).

Now if I could just rename the accounts so they don't all say Inbox (something @ place . com).