The textures on faces inside the model (or outside) when smooth lighting is on, act like the ones that should be at the very edge of the block, for example if the face is facing down, it acts like the one on bottom of the block, the one that would touch the block under it. That means if there is this block under, the texture on the face that doesn't touch this block turns dark like the one that does.
The problem only occurs with smooth lighting on, probably because with smooth lighting off the texture that is hidden by touching block doesn't turn black (but I can't be sure)
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Regression of MC-51447

The end portal issue was actually MC-51113, which was fixed for end portal frames in 15w46a.
The rest of the issues still exist in 15w46a. Properly set cullfaces fixes the darkening on most blocks on fast lighting, but they are not fixed on smooth lighting.

It's still not fixed in 1.9.4.

Is this still an issue in the latest snapshot 16w44a? If so please update the affected versions.
This is an automated comment on any open or reopened issue with out-of-date affected versions.

Is this still an issue in the most recent versions (currently that is 1.11) of Minecraft? If so, please update the affected versions and help us keeping this ticket updated from time to time. If you are the owner/reporter of this ticket, you can modify the affected version(s) yourself.