Is the jumping guy a force user and the normally walking a non-force user?
With JA came indeed this jumping behavior. It has delighted my a couple of times, once in the Team Corellia map and once in my current project, both times with a CLASS_JEDI NPC. It seems they are very precise with their requirements for waypoints and nav_goals. Especially if you are trying to build a route around some low obstacle.
There are two things you can try:
1) Adjust the nav_goals (and supporting waypoint network. Yes, the waypoint network to support nav_goals is of utmost importance in JA). Perhaps try a wider path around the obstacle. Notice that it doesn't need to be a great bulk in between. Some small detail can be quite enough. They jump very easily.
2) Try adding some NPC_noentry or NPC_noenter or whatever was the name of the shader. That might provide you another way to control the paths of the NPCs. Just be aware that it might easily just get the NPC stuck in place, if not used with caution.
Frozen by ICARUS