I ran a git bisect with:

# bad: [291395b47cff7cf1c2ef3f51ea10ff1859888876] UBUNTU: 
Ubuntu-lts-3.16.0-39.53~14.04.1
# good: [991bc91294525e4fb701f2c9a435215b2223d81a] UBUNTU: 
Ubuntu-lts-3.16.0-38.52~14.04.1

I believe the bug was introduced with:

# first bad commit: [07cb1b8e7b70f7a0a0afe4657e9854fe85e1bd23] skbuff:
Do not scrub skb mark within the same name space

I am going to test the upstream kernel and will post the results.

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https://bugs.launchpad.net/bugs/1467561

Title:
  IPsec VTI functionality broken in 3.16.0-39

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  Gentlepeople - this is my very first bug-report to/about Ubuntu, so
  please forgive any failings regarding "form" on my side!

  After upgrading from 3.16.0-38-generic to 3.16.0-39-generic I noticed a 
number of my IPsec VTIs were no longer working:
  All crypto parts appear to work fine (I can run tcpdump on the VTIs and I 
correct cleartext-packets in both directions), but incoming packets are not 
being "processed further" (they are simply ignored). It is like there is no IP 
stack listening on the inbound end of the VTI. I can ping devices on the other 
side and do see the packets w/ tcpdump/wireshark all over the place (locally, 
remote-router, remote-device), the targets respond and I again see the packets 
all the way, but the ping application pretends it never heard or saw a thing. 

  This is true for all VTIs, except those where I put complicated mangle
  and nat rules in place in order to overcome address-space collisions
  (damn RFC1918, damn, damn, damn!!!) - but then again source-NAT
  (masquerading) no longer works on these VTIs either.

  I tested around by leaving *everything* (StrongSwan config, etc.) the
  same and only switching kernels and 3.16.0-38 ist the last one fully
  working and everything after and including 3.16.0-39 is broken in the
  way described above.

  I am willing to test further and dig deeper unless you tell me that it
  is a known problem with an upcoming fix ... :-)

  Thanks, Clemens

  ProblemType: Bug
  DistroRelease: Ubuntu 14.10
  Package: linux-image-3.16.0-39-generic (not installed)
  ProcVersionSignature: Ubuntu 3.16.0-38.52-generic 3.16.7-ckt10
  Uname: Linux 3.16.0-38-generic x86_64
  NonfreeKernelModules: zfs zunicode zcommon znvpair zavl
  AlsaDevices: Error: command ['ls', '-l', '/dev/snd/'] failed with exit code 
2: ls: cannot access /dev/snd/: No such file or directory
  AplayDevices: Error: [Errno 2] No such file or directory: 'aplay'
  ApportVersion: 2.14.7-0ubuntu8.5
  Architecture: amd64
  ArecordDevices: Error: [Errno 2] No such file or directory: 'arecord'
  CRDA: Error: [Errno 2] No such file or directory: 'iw'
  Date: Mon Jun 22 16:48:33 2015
  HibernationDevice: RESUME=UUID=e0eb93cf-68f6-4c6b-b4f1-288db4b33df2
  InstallationDate: Installed on 2015-02-15 (126 days ago)
  InstallationMedia: Ubuntu-Server 14.04.1 LTS "Trusty Tahr" - Release amd64 
(20140722.3)
  Lsusb:
   Bus 001 Device 002: ID 0627:0001 Adomax Technology Co., Ltd 
   Bus 001 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
  MachineType: QEMU Standard PC (i440FX + PIIX, 1996)
  PciMultimedia:
   
  ProcEnviron:
   LANGUAGE=en_US:en
   TERM=xterm
   PATH=(custom, no user)
   LANG=en_US.UTF-8
   SHELL=/usr/bin/tcsh
  ProcFB: 0 EFI VGA
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.16.0-38-generic 
root=UUID=bb995ded-003a-4ae3-aa21-0cf188bdba17 ro
  RelatedPackageVersions:
   linux-restricted-modules-3.16.0-38-generic N/A
   linux-backports-modules-3.16.0-38-generic  N/A
   linux-firmware                             1.138.1
  RfKill: Error: [Errno 2] No such file or directory: 'rfkill'
  SourcePackage: linux
  UpgradeStatus: Upgraded to utopic on 2015-02-15 (126 days ago)
  dmi.bios.date: 01/01/2011
  dmi.bios.vendor: Bochs
  dmi.bios.version: Bochs
  dmi.chassis.type: 1
  dmi.chassis.vendor: Bochs
  dmi.modalias: 
dmi:bvnBochs:bvrBochs:bd01/01/2011:svnQEMU:pnStandardPC(i440FX+PIIX,1996):pvrpc-i440fx-trusty:cvnBochs:ct1:cvr:
  dmi.product.name: Standard PC (i440FX + PIIX, 1996)
  dmi.product.version: pc-i440fx-trusty
  dmi.sys.vendor: QEMU

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