How about the turnaround time at your home base?
And when you say that "50% of my delays have been caused by schedules" is NOT the same as the "probability of delay" what you see ... It means that you have had some delays and half of them are because of the tight a/c scheduling, and the 'probability of delay' what you see in route edit/open view means that this particular flight has the xx% chance of being delayed somewhere during it's route. Two different things. Plus still, even if the delay probability is near 0%, there still can be unexpected things that cause problems.
And looking at the stats of your airline, the average delay of ALL flights has been only 4 minutes, with punctuality 88% which are good figures. So there's nothing strange there in my mind.