@@unknown : I haven't been able to recreate it since yesterday actually. It seems that it only happens in certain circumstances which I've been trying to replicate with no success. It has definitely happened twice, on "old" Nether portals in a world generated in a previous 1.9 snapshot. Will update with more information if it happens again.
This bug is still occurring in 15w42a SMP, occasionally. I find that when my connection is slower (when uploading/downloading something outside of MC) it happens.
Can confirm it happens in 15w43a, fresh randomly generated world.