Ok, so this proves my point. The unwanted "change" somewhere in the X/GL
stack is that the visual with the composite alpha channels is now
"accidentally" chosen by default whereas the applications expect the
alpha channel to be ignored.

I just decompiled Minecraft and hacked the calls to glClearColor to set
the alpha value to "1.0" and this "corrects" the output (at least for
Minecraft...).

gcc -o test test.c -lX11 -lXrender -lGL && ./test

Prints:

visual 0: alphaMask = 255
visual 1: alphaMask = 0
visual 2: alphaMask = 0
visual 3: alphaMask = 0
visual 4: alphaMask = 0
visual 5: alphaMask = 0
visual 6: alphaMask = 0
visual 7: alphaMask = 0

Which means that the first visual proposed contains the alpha mask
causing unwanted alpha compositing.

** Attachment added: "GLXFBconfig alphaMask dump: gcc -o test test.c -lX11 
-lXrender -lGL && ./test"
   
https://bugs.launchpad.net/ubuntu/+source/xserver-xorg-video-intel/+bug/1277905/+attachment/4015392/+files/test.c

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https://bugs.launchpad.net/bugs/1277905

Title:
  Game windows (minecraft, titan attacks, maybe others) on Intel are
  transparent and no longer playable

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