I too am having this problem. Did anyone find a solution?
To be clear, Teleport to Waypoint works sometimes but it's very unreliable and I'm not sure what is making it not work. At this point I just use it to unlock towers. Teleport 100 units above the tower and you fall right on top of it so there is no messing with bugged or glitchy controls as you try to climb up some of the harder towers.
Anyway, since I've reached the southern island I have been unable to get it to work. I've tried reloading the game, relaunching the trainer, activating nothing else but the waypoint and the teleport, activation from multiple locations to multiple waypoints, etc. Not sure what's going on.
I'm open to alternatives also if anyone can suggest something. Air Runner doesn't work around the towers, they appear to block approach from the air. No clue what Air Jump does as it's never worked for me. Super Jump works great but it doesn't jump high enough to be useful for the towers. Ideas appreciated.