An unofficial (and unacceptable) fix that finally worked for me was.... to 
switch to Linux Mint 17.1. 
It is based on Ubuntu 14.04 LTS, so I wonder what they did better, particularly 
because they seem to be using exactly the same X org and  graphics driver 
versions. 
X.org 1.15.1
Nvidia: 331.113

Not sure of xorg, but nvidia is definitely from the Ubuntu repos.

Things that work correctly now:
- booting the system with the second monitor plugged in
- no strange temporary artifacts/glitches when changing graphics mode during 
startup of the x session (however, it also takes *longer* for mint to display 
the desktop, than for Ubuntu)
- booting the system with the laptop lid closed (!) by pressing the docking 
station power button and using only the big secondary screen (last time I 
checked this with Ubuntu, I got a permanent system freeze and both screens 
black)
- plugging/unplugging the laptop multiple times from the docking station with 
external monitor turned on 
- suspending/hibernating, undocking, resuming (it picks up the new screen 
config after resume just fine)
- suspending/hibernating, docking, resuming

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https://bugs.launchpad.net/bugs/1382462

Title:
  Desktop/windows painted incorrectly in dual monitor configuration

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