El Capitan sidebar preferences not sticking
I knew something was fishy with my home folder. I used the procedure here https://appletoolbox.com/fix-corrupt-user-accounts-macos/#Reset_Home_Folder_Permissions to reset the permissions on my home folder (note: the El Cap-specific directions didn't work, but the directions provided for Sierra and above did) and the problems I've been having with various things not sticking, including sidebar appearance and trackpad preferences seem to have gone away.