Mario,
I found the issue. I am running 4.6.0-040600rc4-generic from testing in my bug 
report. I had install jsalisbury's kernel but was not booting into it. I hit 
GRUB on the reboot and booted into 4.4.0-21 which matches his kernel.

I get this now for uname -a:
Linux yeti 4.4.0-21-generic #37-Ubuntu SMP Mon Apr 18 18:33:37 UTC 2016 x86_64 
x86_64 x86_64 GNU/Linux

But hotplug does not work still. Again, I still could be screwing up
changing up the kernels, so take with a large grain of salt.

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https://bugs.launchpad.net/bugs/1577898

Title:
  thunderbolt hotplug is broken

Status in linux package in Ubuntu:
  In Progress
Status in linux source package in Trusty:
  In Progress
Status in linux source package in Vivid:
  In Progress
Status in linux source package in Wily:
  In Progress
Status in linux source package in Xenial:
  In Progress
Status in linux source package in Yakkety:
  In Progress

Bug description:
  Thunderbolt hotplug is broken on type-c ports.  Redhat already
  submitted a patch for this that was accepted into upstream ACPICA, but
  it needs to be backported into Ubuntu's kernel.

  I've verified that the patch works properly using a type-C USB
  Ethernet dongle as well as hot-plugging a Dell TB15 dock.

  http://www.spinics.net/lists/linux-acpi/msg65578.html

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