Do you happen to be toggling filters, perhaps accidentally? (I would doubt it, as that would likely disable ALL fast travel points, not just some.) But, such weirdness could be due to:
Ive uninstalled and reloaded mods, it solved for a few playsthroughs, then began to disappear again.
That is most likely the answer right there. Once a game is saved with mods running, the reference data from those mods will forever be in the save state. Removing mods can actually introduce issues, as the associated reference data now points to nothing.
If you used any sort of mod that altered or added in any way to the fast travel system, it's possible that it's not fully updated to be compatible with the latest version of the game.
I can't be sure, of course, but I don't remember ever coming across this issue before. (People not being able to find them, or new ones not appearing, yes. Existing ones disappearing, no.)
