Still no responses from earlier posts, so now I just post data, and hope it's not issue -- If is, I'll delete.
Rata Sum Missing POI -354.99, 27.22, 117.19 (Will test on new toon if this works EDIT: Confirmed, worked on new toon. Bypassed story instance, and still got POI)
Black Citadel Missing POI 56.95, 259.13, 204.32 (Worked on toon that was missing it EDIT: This too worked, but for some reason the Z was too high, so the end coords became: 56.95, 259.13, 196.51)
Also, can I help you rename some waypoints and such so they are easier to find? For instance Trader's Forum is oft teleported to in LA. Reason I like your program is cuz it has no loading screen for it. So I prefer to wp with midnight, than in game.
Another one that is missing is the dock man at South Sun Cove as well as from LA. I often am miserly and save money by going to that guy to teleport between rich ori node and LA.
Though these are close to WPs too, so not too bad If not added:
Southsun Cove Transport Facilitator (LA) -252.15, -54.22, 14.72
Sailor (Point Lion, Southsun Cove) -21.55, 497.55, 8.51