NPC AI Kit- Waypoint Patrol Issue

So with the new animated mesh system I decided to go through and update all of my NPCs and spawners with the new meshes and the most recent version of the NPC AI Kit. I replaces waypoints and updated all of the NPC scripts and the Combat Dependencies to the newest versions. Now, for some reason, all of my patrolling NPCs are either walking through the air or through the hills in the terrain. They didn't do this before. Have I missed something?