On any fast extending piston elevator setup on halfslabs you never touch the ground while going upwards resulting in accumulating falldamage, as seen here http://youtu.be/snyRGMOnZh8?t=2m24s
One Possible solution to this and many other bugs related to fall damage would be to make the fall damage only depending on the vertical velocity an entity has when hitting a solid surface,or to reset the fall height when being moved upwards by a piston.
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Attached a Worlddownload of some elevator demo setups now! The video is still uploading, that is why it is private, it will be available soon!
OK, sorry.
Does this happen just when it goes down?
I take damage when it goes up occasionally, but not when it goes own.
It might be a glitch with the slime blocks. every so often they can launch you upward. This is related to another glitch where your walking speed is slowed if certain blocks are placed over slime blocks or you slide when those blocks are placed on ice. For a temporary fix, try using a solid block instead of slabs. It might be inconvenient, but it should no longer cause the fall damage hopefully.
The world save was helpful for testing the glitch.
Duplicate of MC-62492
why give a link to a private video? also, can you post a screenshot of the piston setup?