I came across this bug - I've cherry-picked the patch and uploaded it.

Let this bug know if it doesn't work (once it's been automatically
closed).

** Changed in: gvfs (Ubuntu)
       Status: Triaged => Fix Committed

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https://bugs.launchpad.net/bugs/1618370

Title:
  nautilus does not show external drives in sidebar if plugged in on
  reboot

Status in Nautilus:
  Unknown
Status in gvfs package in Ubuntu:
  Fix Committed

Bug description:
  nautilus 3.20 should show external drivers in its sidebar (I believe
  this is the case since 3.19). It always shows my SD card drive in the
  sidebar, but it only shows external USB drives in the sidebar if I
  plug them in once I have logged into the desktop. If they are plugged
  in during a reboot and I log in, they only appear in 'Other Locations'
  (and the SD card does not appear there; I don't know if that's a bug
  or not).

  If I unmount the external drives and remount them, they still only
  appear in 'Other Locations'. I have to unmount them, remove them and
  plug them back in for them to appear in the sidebar.

  The attached shows nautilus with 3 drives plugged in. The SD card
  appears in the sidebar, but the USB drives (a btrfs and another with a
  btrfs and a ntfs partition) only are in 'Other Locations'.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.10
  Package: nautilus 1:3.20.2-0ubuntu1
  Uname: Linux 4.7.2-040702-generic x86_64
  ApportVersion: 2.20.3-0ubuntu7
  Architecture: amd64
  CurrentDesktop: Unity
  Date: Tue Aug 30 17:03:44 2016
  GsettingsChanges: b'org.gnome.nautilus.window-state' b'geometry' 
b"'890x550+65+24'"
  InstallationDate: Installed on 2016-07-04 (56 days ago)
  InstallationMedia: Ubuntu 16.04 LTS "Xenial Xerus" - Release amd64 
(20160420.1)
  JournalErrors:
   Error: command ['journalctl', '-b', '--priority=warning', '--lines=1000'] 
failed with exit code 1: Hint: You are currently not seeing messages from other 
users and the system.
         Users in the 'systemd-journal' group can see all messages. Pass -q to
         turn off this notice.
   No journal files were opened due to insufficient permissions.
  SourcePackage: nautilus
  UpgradeStatus: Upgraded to yakkety on 2016-07-24 (36 days ago)

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