Sorry for the late reply, I didn't get any notifications of your
response. After I reported this issue there were a couple of updates to
ZFS. This problem never occurred again, and there were several updates
that redid initramfs, kernel, etc..., with the pool being imported and
mounted. Didn't have to mark it for no cachefile either.

Looks to me this is fixed.

* zfsutils-linux-0.6.5.6-0ubuntu14
* Linux erebus 4.4.0-36-generic #55-Ubuntu SMP Thu Aug 11 18:01:55 UTC 2016 
x86_64 x86_64 x86_64 GNU/Linux

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https://bugs.launchpad.net/bugs/1624844

Title:
  Ubuntu 16.04 breaks boot with wrong zpool.cache

Status in zfs-linux package in Ubuntu:
  Incomplete

Bug description:
  Having just upgraded Ubuntu 16.04, and seeing systemd updates, I
  rebooted the machine, but it failed to start, entering emergency mode.
  Relevant piece of info was this:

  * Failed to start Import ZFS pools by cache file.
  * Started Mount ZFS filesystems
  ** A start job is running for dev-disk....

  and then it enters emergency mode.

  Now, the only ZFS pool I have is a backup USB HDD which is constantly
  attached, and the pool is on a LUKS provider, meaning you won't see it
  until the provider is unlocked.

  My guess is that the latest update, having triggered initramfs
  rebuild, wrote the zpool.cache file with that state, and it shouldn't
  have.

  This is totally wrong, as zpool cache should not be built like this as
  it PREVENTS you from having external pools that might not be available
  on boot. I also have no idea why it happened now because I've been
  having this setup (external backup zfs pool on a LUKS provider) since
  16.04 came out and never had a problem until now.

  Removing the /etc/zfs/zpool.cache allowed the system to reboot fine.

  # lsb_release -rd
  Description:  Ubuntu 16.04.1 LTS
  Release:      16.04

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