If you walk through a nether portal you spawn at the correct location in the nether but no portal is generated or if there is already a portal in range it is not linked. Same bug appear in opposite direction Nether => normal world.

Everything works fine on the default map with the default nether.

I tried different setups, making the worlds in multiverse, importing a complete working set. Linking them via 'mvnp link', no linking, ...
Nothing seems to work.

Me too. How to fix it?

I also have this issue, It will also let you swan into lava lakes too!
Paper spigot 1.12.2
MV-core 2.6.0-snapshot-b736
MV-NetherPortals 2.5.2-snapshot-b728

Having this issue as well.
I created a _nether world and a gateway in the normal world only to end up inside the ground. The spawn location was consistent so I set up a gate in the Nether at the approximate location for 2-way travel. It works, though returning to the normal world doesn't spawn me quite in the right place. Good enough to work with but clearly the mechanics are broken.

Closing issue because it's an old post. If you are still running a Minecraft server and this persists, try updating all the Multiverse plugins and try again, otherwise please don't hesitate to ask for support on our Discord (quickest support) or submit a new issue.