I have one portal in my current snapshot world that causes me to take damage when I leave the nether (between 1-5 hearts). The other portal in the same world doesn't have this issue and it doesn't happen when I go to the nether. I have tested this on Mac and Windows also, but the problem doesn't happen on those systems.
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It looks like the issue is with the Open JDK (the default on OpenSUSE). I tried running it on Linux with Oracle's java 1.8.60 and the issue doesn't appear to be present.
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Nevermind, it happens with Oracle's java also, but it deals less damage. The most I've taken there so far is 1 heart.
It is also still present in 15w43a.
This doesn't look like the same issue as MC-89928.
For one, this issue only happens on Linux, not on Mac or Windows.
The other reason, is my coordinates appear to be correct. The portal I have that causes the problem is at (66,72,-168) in the normal world and (-5,68,-6) in the nether. The other portal I have in my world that does not have this problem is at (763,68,-57) in the normal world and (95,68,-6) in the nether.
I don't mind attaching the world, but it is a little to big to attach (18.4 Mb zipped).