I have a similar issue with ubuntu® 16.04.1:  My own system recently
hung attempting to initialize not more than two of five swap partitions
("[<---->] A start job is running for dev-mapper-cryptswap?.device
(??m??s / No limit)") on several attempts and subsequently hung on
unattended-upgrades on attempted reboot.  Disabling cryptswap worked
around the problem.  The hang-on-startup problem initially appeared to
be centered on hit-and-miss automatic key generation for ecryptfs; but
the unattended-upgrades problem is simultaneous.  Don't yet know if I've
this Bug (viz., #1594035) in specific, or have to file a new Bug, as of
6 December 2016; the answer depends on replies to Question #404663,
opened 5 December.

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https://bugs.launchpad.net/bugs/1594035

Title:
  unable to shut down the system after suspend / resume

Status in systemd package in Ubuntu:
  Confirmed

Bug description:
  In the case of a system that has gone through a suspend / resume
  cycle, the "shutdown now" command fails with the following output:

  $ shutdown now
  Failed to power off system via logind: Transaction is destructive.
  Failed to start poweroff.target: Interactive authentication required.
  See system logs and 'systemctl status poweroff.target' for details.
  Failed to open /dev/initctl: Permission denied
  Failed to talk to init daemon.

  ---

  $ systemctl status poweroff.target
  ● poweroff.target - Power-Off
     Loaded: loaded (/lib/systemd/system/poweroff.target; disabled; vendor 
preset:
     Active: inactive (dead)
       Docs: man:systemd.special(7)

  ---

  $ systemctl list-jobs
  JOB UNIT                                  TYPE  STATE  
  438 dev-mapper-cryptswap1.device          start running
  439 dev-mapper-cryptswap1.swap            start waiting
  436 systemd-cryptsetup@cryptswap1.service start running

  3 jobs listed.

  ---

  Steps to reproduce:

  1. Boot system
  2. User login to graphical session
  3. Close lid while on battery power triggering a suspend
  4. Open lid while on battery power triggering a resume
  5. Run "shutdown now" from a terminal. Note that the command must be run from 
the terminal to see output. Selecting "Shut Down..." from the system menu in 
the menu bar will hide the error output.
  6. Observe that the system fails to shut down

  Expected behavior:

  At step 6, the system should shut down gracefully.

  Note that the shutdown process works as expected if steps 3 and 4 are
  skipped. I suspect that something about the suspend / resume cycle
  during the session has an interaction effect with the shutdown
  process, preventing it from executing correctly.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: systemd 229-4ubuntu6
  ProcVersionSignature: Ubuntu 4.4.0-24.43-generic 4.4.10
  Uname: Linux 4.4.0-24-generic x86_64
  ApportVersion: 2.20.1-0ubuntu2.1
  Architecture: amd64
  CurrentDesktop: Unity
  Date: Sat Jun 18 18:04:26 2016
  EcryptfsInUse: Yes
  Lsusb:
   Bus 002 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
   Bus 001 Device 003: ID 04f2:b550 Chicony Electronics Co., Ltd 
   Bus 001 Device 002: ID 8087:0a2a Intel Corp. 
   Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
  MachineType: System76, Inc. Lemur
  ProcEnviron:
   LANGUAGE=en_US
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.4.0-24-generic.efi.signed 
root=UUID=7aecd352-8a3f-4ce9-88b8-0fc048dc9660 ro quiet splash vt.handoff=7
  SourcePackage: systemd
  UpgradeStatus: No upgrade log present (probably fresh install)
  dmi.bios.date: 11/29/2015
  dmi.bios.vendor: American Megatrends Inc.
  dmi.bios.version: 1.05.06RS76
  dmi.board.asset.tag: Tag 12345
  dmi.board.name: Lemur
  dmi.board.vendor: System76, Inc.
  dmi.board.version: lemu6
  dmi.chassis.asset.tag: No Asset Tag
  dmi.chassis.type: 10
  dmi.chassis.vendor: System76, Inc.
  dmi.chassis.version: N/A
  dmi.modalias: 
dmi:bvnAmericanMegatrendsInc.:bvr1.05.06RS76:bd11/29/2015:svnSystem76,Inc.:pnLemur:pvrlemu6:rvnSystem76,Inc.:rnLemur:rvrlemu6:cvnSystem76,Inc.:ct10:cvrN/A:
  dmi.product.name: Lemur
  dmi.product.version: lemu6
  dmi.sys.vendor: System76, Inc.

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