I have the latest 1.9.2 Spigot server running the latest Jenkins build (March 12) of Multiverse-Portals. 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.

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

Sorry, I reported this on the wrong plugin. It's a MV-NetherPortals issue.