It takes me to the correct dimension, but not the correct coordinates. This test even placed me in solid stone underground. It appears to be able to target the proper dimension, but doesn't change the player's current coordinates.

Example case:

Target [Overworld]

Starting Point [Twilight Forest]

End Point [Overworld]

This is not happening to me, what other mods do you have installed?

It seems it isn't happening anymore, although now my Twilight Forest portal is doing something similar (putting me underground when I come back).

Mod List: https://hastebin.com/fibahanuvu.css

It's likely some other mod causing the problem then (maybe even Twilight Forest itself), Waystones wouldn't be able to alter the Twilight Forest portal behaviour. Could also try temporarily disabling other mods that may alter teleportation behaviour and see if you still have issues (e.g. NetherPortalFix, though I doubt it's related).

It's working now, no idea why since I didn't change my mod list. Well, whatever. If I get this issue again I'll try to narrow it down, then re-open the issue.