I can reproduce this with minecraft, seems to be the case indeed.

The same binary on saucy on a snb:
visual 0/51: 24 depth, RGB: ff ff ff alphaMask = 0
visual 1/4d: 32 depth, RGB: ff ff ff alphaMask = ff
visual 2/51: 24 depth, RGB: ff ff ff alphaMask = 0
visual 3/51: 24 depth, RGB: ff ff ff alphaMask = 0
visual 4/51: 24 depth, RGB: ff ff ff alphaMask = 0
visual 5/51: 24 depth, RGB: ff ff ff alphaMask = 0
visual 6/51: 24 depth, RGB: ff ff ff alphaMask = 0
visual 7/51: 24 depth, RGB: ff ff ff alphaMask = 0

trusty:
visual 0/4d: 32 depth, RGB: ff ff ff alphaMask = ff
visual 1/51: 24 depth, RGB: ff ff ff alphaMask = 0
visual 2/51: 24 depth, RGB: ff ff ff alphaMask = 0
visual 3/51: 24 depth, RGB: ff ff ff alphaMask = 0
visual 4/51: 24 depth, RGB: ff ff ff alphaMask = 0
visual 5/51: 24 depth, RGB: ff ff ff alphaMask = 0
visual 6/51: 24 depth, RGB: ff ff ff alphaMask = 0
visual 7/51: 24 depth, RGB: ff ff ff alphaMask = 0

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You received this bug notification because you are a member of Ubuntu-X,
which is subscribed to mesa in Ubuntu.
https://bugs.launchpad.net/bugs/1277905

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

To manage notifications about this bug go to:
https://bugs.launchpad.net/ubuntu/+source/mesa/+bug/1277905/+subscriptions

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