I've heard a lot of complaints from frustrated users because Outlook 2013 (and Outlook 2016) keeps changing the sort order of the folders in the Favorites list. The user has the folders arranged in a specific order and Outlook decides to reorder the folders. It's happened to me too, and yes, it's annoying.
With a little trial and error testing, several users discovered the problem seemed to be related to the IMAP folders in the Favorites. They discovered that just leaving the IMAP folders at the bottom of the Favorites list seems to fix the problem, and the remaining folders stay in the desired position.
Opening a new Outlook window should fix it as well. After Outlook opens, right-click on a folder and choose Open in new window. Close the original Outlook window.
If your sort order changed because Outlook crashed and restarted, close Outlook and restart. This always brings back my original sort order.