Many users, myself included, are annoyed by Favorites on the Navigation pane rearranging itself in Outlook 2013 (and newer).
It didn't take me long to figure out at least part of the problem was due to opening my Exchange mailbox on different computers, with different email accounts in the profile. Navigation pane information is stored as a hidden file in the mailbox and travels with the mailbox. But when the profiles are not identical and folders from the missing accounts are on the Favorites list, Favorites is rearranged when the account is opened on the computer with all of the accounts in the profile. Closing Outlook and reopening it often resorts the Favorites to the original order.
Several users discovered another cause: folders from IMAP accounts on the Favorites list. If there are problems connecting to the IMAP account, Outlook waits to add the folders from the IMAP account, resulting in reshuffled Favorites.
There are two solutions:
Put IMAP folders and folders from accounts that aren't in all profiles at the bottom of Favorites and the reshuffling is reduced. While it's annoying to have your folders arranged the way Outlook wants, instead of the way you want, it's less annoying than having the folders rearrange themselves frequently.
If you don't want the IMAP folders at the bottom of the Favorites list, try this solution instead: Right click on a folder and select Open in New Window. A new window opens with the folders sorted correctly. Close the previous window with the sort issue.