I have the latest 1.9.2 Spigot server running the latest Jenkins build (March 12) of Multiverse-NetherPortals and Multiverse-Core. However, the interdimensional teleportation has been causing players great grief.

Whenever you use the nether portal, players sometimes take half-a-heart of damage before appearing on the other dimension of the portal. When the worldborder of the nether world is smaller than the one in the overworld, and when the overworld portal is outside of the border range of the Nether, the player "will suffocate in a wall" before appearing at what it seems like a right location--dead. The temporary solution to this is setting the worldborder damage per block to 0. Also, it seems like the similar problem is causing all the entities that goes through the nether portal to not appear on the other side, but I have yet to test where the entities land after going through the portal.

However, the case with the End is much more extreme. When players use the End portal, they spawn in the End at the wrong coordinates--that is, the same coordinates the player used to enter the end portal back in the overworld (and sends them deep into the void). That happens very often when there's nobody in the End (or maybe when the spawn chunks in the End are not loaded). When there's someone already in the End, the player correctly spawns on the spawning platform. Also, when players use the End portal in the End, they spawn in the x-z coordinates (0,0) of the overworld, regardless of the world's spawn point. All three worlds have the flag "keep-spawn-in-memory"(or similar) set to true.

EDIT: Move the End "spawn point" to the area around/above the End spawning pad. This will keep the chunks around the pod area loaded instead of the middle of the End.

All those symptoms happen in the second survival world. The default world doesn't show these problems. Can they be fixed?

I can confirm that this is occurring with the latest version of Multiverse-NetherPortals when paired with worldborder.
I have my overworld and nether on a 1:3 ratio, and the worldborder set accordingly.
It appears that while the exit nether portal is spawning at the correct coordinates, the player is teleported to the coordinates on a 1:1 ratio, putting them outside the worldborder.
Worldborder detects they are outside the border, and teleports them to the worlds spawn, which in my servers case was set to 0, 0, 0 by default, causing them to fall out of the world and die.
If I put a worldborder bypass on myself and walk through the portal, I come out where the exit portal spawns at the correct coordinates.
The only thing I can assume is happening is the player is being sent to a 1:1 ratio location first, before being sent to the correct coords?
I have not tested this with the end world yet, but I presume from the ops post, that the same issue will occur.

The case with the End portal was the matter of setting the End's spawn point right around the spawning pad.