First off I am new here and do not mean to overstep my bounds but I figured out something that may be key in Waypoints not working.
It doesn't work in a 1280x1024 configration.
I have since tried every other widescreen and fullscreen resolution and it works, but it does not work under any configuration at 1280x1024.
Hope this helps those of you, like me, experiencing the problem. I recommend 1280x960 til it is fixed as it is working for me there.