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After apt-get update && apt-get upgrade, I started seeing black boxes around windows and/or instead of whole windows. Ubuntu is halfway unusable for me.

Example: this is how file browser looks like

first picture

This is how system setting looks like

system settings

And, perhaps most importantly to me, this is how both Terminal and Terminator looks like. (Yes, just a black square.) I work in Terminal and it is my basic work tool. Now, Ubuntu update (??) made my computer completely unusable for work.

terminal

All system notifications are black squares. The menus on the top bar are surrounded by black squares.

I will copy whatever information needed (even when it is hard without access to terminal, but I can use ctrl-alt-f5 & redirecting & text editor).

Booting to an older kernel does not fix the issue.

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    Please include details about your system, especially your graphics card. – TheSchwa Mar 6 '16 at 22:50
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    what is your GPU? were you using a OEM driver? This looks like an inadequate video memory issue. show $ sudo lshw -c display – j0h Mar 6 '16 at 22:51
  • I fixed it by upgrading all "held back" packages, see below my own answer. Should I still paste the info though? – Karel Bílek Mar 6 '16 at 22:51
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Upgrading all the apt packages that have been "held back" actually fixed the issue.

To be exact,

sudo apt-get upgrade libgl1-mesa-dri libgl1-mesa-dri:i386 libxatracker2

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