After further investigation ;) and testing the problem seems a little
bit more clear.

We've installed windows 2012r2  on the same server to be sure not having
a potential hardware problem - !! On windows the  same problem exists !!

Than we changed the switch. At first, there was a netgear 8port
unmanaged switch to a netgear 8+2port managed switch. No problem on
windows neither a problem on linux with the managed switch (Release
Notes Intel Driver - potential problem with unamanaged switches).

No plug/unplug problem, no lost packets and not a wrong packet counter
anymore.

So all fine ? ... allmost

The wrong packet counter and some of the misbehaviour on plug/unplug and
also lost packets seems to come FROM THE SAME NETWORK ON BOTH INTERFACES
!!

Problem configuration 1:
eth0 192.168.86.11/24
eth0:0 172.22.1.81/24

dhcp:
eth1 172.22.1. 243/24

ping test to 172.22.1.81 and 172.22.1. 243
------------------------------------------------------------------
Problem configuration 2:
eth0 172.22.1.81/24

dhcp:
eth1 172.22.1. 243/24

ping test to 172.22.1.81 and 172.22.1. 243
------------------------------------------------------------------
Working configuration:
eth0 192.168.86.11/24

dhcp:
eth1 172.22.1. 243/24

ping test to 192.168.86.11 and 172.22.1. 243

... so there seems to be a general bug left in network stack/logic of
the kernel ...

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https://bugs.launchpad.net/bugs/1370018

Title:
  igb driver does not initialize network cards - no link intel I210
  rev03

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