Raphael:
I've noticed something similar with versions of the Mission Editor since 2.13.1. Earlier versions were better.
Here is what I've noticed:
During offline missions, if you watch the map, you'll see a triangular marker that follows the mission plan. It advances across the map, and seems to be indicating where your mission plan INTENDED for planes to be located at that point in time. In earlier versions of the Mission Editor and Aces High, the bot planes followed that moving indicator quite closely.
However, with later versions like those now in popular use, the planes get delayed. Usually this comes about due to the oft-mentioned "slower than scripted" flight. However, in your case the problem may be made even worse by the 5 minute delayed departure. In either event, when the bots are off course, they seem to fly toward that moving indicator. Now, if the moving indicator happens to be straight ahead of their current course, you won't notice the effect. But if the moving indicator is off to the side due to a course change that your bot SHOULD already have encountered, then the bots may depart SIGNIFICANTLY from the scripted course, taking a "shortcut" toward the scripted location. In my recent experience, the bots rarely actually catch up with the scripted course, so they are always wandering through this "shortcut" logic.
Keep in mind that this is just my unscientific observation. It may or may not be accurate even in my case, and it may or may not explain what you are seeing. But it might....