I had this glitch since I started my new world in the 1.9 pre 2 version. Basically I suffered 1 or 2 damage points every time I went to the nether and almost 18 points when I went back to the over-world.

The temporal fix that I found, is that you can use the portal in the nether's coordinates in the over-world, make a big hole there (like 6x6x6) and then do the same in the nether with the over-world portal's coordinates.

I hope this helps someone else!

This happens because when you take the portal, you would get in the same coordinate (but different world) for a bit and then you would be moved to the portal exit. So if there are blocks there you would be suffocated, ESPECIALLY if you have bad connection to the server.