Thank you for your reply. You are right about the contract sections. I have re-read the contract. This is what it says:
•Make sure your craft is made especially for ...
•Flyby Jool
•Flyby Laythe
•Flyby Dres
...
No any special altitude, trajectory or inclination.
The 'Make sure' section always stays green, the flyby Jool and flyby Laythe sections turn black after approximately 1.5 years (the time I am flying to Dres) and this is quite strange, because I am way too far away from Jool all the time, but for some reason it just decides to turn black randomly. I have reloaded quite a few times, and this happens sometimes earlier, sometimes later.