Odd. Can I get a small screenshot of the section in question (with waypoints)?; I'm not quite sure I understand the layout of the terrain you're working with.
If a bot keeps jumping, that indicates that it missed the initial "jump" waypoint. Put down guards around the target waypoint in case it misses like that (which can result just from combat, collecting disruptive power-ups, or even just random behavior—bots don't obey perfectly every time, which I think MM purposely coded so they would have variation in movement).
This pic. probably does not detail the exact sector in mind, but shows the functional use of guards:
Note how the jump waypoint is not directly above the run-left, at the bottom. Go ahead and try in-game yourself; if you jump vertically as SOON as you stop running, the soldat still continues to drift forward a bit.
Guards become of exceptional use if you're getting bots to fly over long distances, where their paths become more and more unpredictable