I have got a problem with the Pilot Focus: On every change of influence the boni get lost. For example: I am on the launchpad and it shows all the additional navigation options next to the navball, i start the rocket and they are gone. So i quickly eva to get them back. Then on leaving the atmosphere the same thing happens. And again on entering orbit, etc. I am not shure if it affects the rewards as well. When i did tourist missions and i had it on Pilot Focus II i got 50% instead of 100% to rewards, on Pilot Focus III it was ~75% instead of 200%. I mean from a balancing standpoint it is alright, but maybe thats not the way it was intended.
Oh and i think i had the same issue with the Scientist Focus. The additional stars went missing like they do now and i had to eva to get them back. I didnt really pay attention to the boni - they may have been affected as well.