The apparent cause seems to be lvm2 (2.02.133-1ubuntu8). From the
Changelog (https://launchpad.net/ubuntu/xenial/+source/lvm2/+changelog)

lvm2 (2.02.133-1ubuntu8) xenial; urgency=medium

  * Drop debian/85-lvm2.rules. This is redundant now, VGs are already
    auto-assembled via lvmetad and 69-lvm-metad.rules. This gets rid of using
    watershed, which causes deadlocks due to blocking udev rule processing.
    (LP: #1560710)
  * debian/rules: Put back initramfs-tools script to ensure that the root and
    resume devices are activated (lvmetad is not yet running in the initrd).
  * debian/rules: Put back activation systemd generator, to assemble LVs in
    case the admin disabled lvmetad.
  * Make debian/initramfs-tools/lvm2/scripts/init-premount/lvm2 executable and
    remove spurious chmod +x Ubuntu delta in debian/rules.

 -- Martin Pitt <martin.p...@ubuntu.com>  Wed, 30 Mar 2016 10:56:49
+0200


The initramfs-tools script does not activate all of the logical volumes and its 
detection is lacking in certain edge cases like mine.

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https://bugs.launchpad.net/bugs/1573982

Title:
  LVM boot problem - volumes not activated after upgrade to Xenial

Status in lvm2 package in Ubuntu:
  Confirmed

Bug description:
  Soon after upgrade to Xenial (from 15.10) the boot process got broken.
  I'm using LVM for /root swap and other partitions.

  ===
  The current behaviour is:

  When I boot short after the Grub login screen I'm getting log messages
  like:

  ---
  Scanning for Btrfs filesystems
  resume: Could not state the resume device file: '/dev/mapper/VolGroup....'
  Please type in the full path...
  ---

  Then I press ENTER, for a few minutes some errors about floppy device
  access are raised (for some reason it tries to scan fd0 when floppy
  drive is empty). And then:

  ---
  Gave up waiting for root device. Common problems: ...
  ...
  ALERT! UUID=xxx-xxx.... does not exist.
  Dropping to a shell.
  ---

  From the BusyBox shell I managed to recover the boot by issuing "lvm
  vgchange -ay", then exit and then boot continues fine (all LVM file
  systems are successfully mounted).

  ===
  One workaround so far is creating 
/etc/initramfs-tools/scripts/local-top/lvm2-manual script doing "lvm vgchange 
-ay". But I'm looking for cleaner solution.

  Boot used to work fine with 15.10. Actually the first boot after
  upgrading to Xenial actually worked OK too, I'm not sure what might
  changed meanwhile (I've been fixing some packages installation since
  mysql server upgrade has failed).

  ===
  # lsb_release -rd
  Description:  Ubuntu 16.04 LTS
  Release:      16.04

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