So, i've been doing a lot of missions for the logos. And every time i meet their ship they seems super happy with me doing missions for them, yet when i fly away a message always pops up that "you've lost respect with the logos".

Basically it goes like this:
They rush after you and an encoutenr beings.
They hail you - and give you a mission
I fly away from the encounter - message pops up when i enter the planetary screen that "you've lost respect with the logos".


I noticed that once they rush after you and give you a mission. (The encounter then starts and you are hailed)
When you hail their ship again without flying away from the encounter, they want to go through the "we want to inspect your cargo routine". And after you go through it they fly away themselves - so i was hoping that this way i would not lose reputation with them, however the message still popped up. (albeit that time i had an infested crew member who then got cleansed on the 2nd transmission).

I will try to reproduce one more time without the infested crew if possible, and see if it still happens.