This is surely old news to most of you, but hey, maybe it will help a few people.

When I first started playing, I didn't bother to name systems because I figured it would be too much trouble. THEN I realized it's really helpful for remembering places you might want to return to.

Problem is, my custom names weren't showing up in the list of terminus stations in the teleporter. It still showed the original system name. So if I wanted to go back to "Eden Prime" or whatever, I had to remember which it was, making naming pointless.

THEN I realized that if you named the system BEFORE visiting a space station, the station would have your custom name when you visited, and in turn the custom name would show up in your list of terminus destinations.

Okay, cool. So name systems right away so the name attaches to the space station.

I like to name a system with something that reflects its character, though, so that still presented a problem, since I like to get some missions before going to the planets. A small problem, but a problem all the same.

THEN I realized that a station will rename itself after your name if you revisit it. This works even for systems you left behind.

In other words, you arrive in Ozikark VI and go to the station, it will be the Ozikark VI terminus and that's how it will show up in your list of teleport destinations. If you leave the station, rename the system "Meshedsabre's Discovery," and return to the station, the station will rename itself and the new name will show up in the teleport destinations.

You can teleport back to old systems with incoherent names, fly out real quick, turn around, go right back in, and your new name will then replace the old one in the list of 'port destinations.

Again, I'm sure this is very obvious to most of you and I'm way way behind, but I only JUST discovered it after 80 hours of play. D'oh!!

TL;DNR – Your list of terminus destinations in the teleporter uses whatever the system was named the last time you flew into the system's space station. If your custom name isn't showing up in your list of destinations, go back to the station, fly out, then fly back in. It should change the station name to your custom name.