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Confirmed for 1.8.2-pre1.

Ticket resolved as incomplete, because no answer in a reasonable amount of time (1+ year), if it still happens, please update the ticket.

This is still an issue even in the latest 1.12 snapshot, 17w06a.
But I think this issue is exclusive to chickens (or any other mobs that have their eye height right at the top of their bounding box).
I think this happens because when they jump up against the ceiling, since their eye height is at the top of their hitbox, their head is then considered to be inside the ceiling block and thus they take suffocation damage. You can achieve the same for example by pushing them against a ceiling with a piston or a shulker box.
This is still an issue in 14w30c.
This happens when chickens or baby cows (at least) jump up from non-full blocks such as carpets, redstone repeaters, daylight sensors and a few sheets thick snow into a one block high gap. They take suffocation damage from the ceiling. It might be because their eye level seems to be just above their collision box❓ (F3+B). It doesn't affect baby pigs, probably since their eye level is noticeably lower. Here is an example of an automatic chicken suicide booth: http://imgur.com/zvTBnje