I also do mostly medium cargo in a Caravan and the lowest score I ever got on airline procedures was 75% (and I’m still not sure if it was because I cancelled to VFR before ATC told me so or for some deviation from requested altitude).
I was able to fix the issue by verifying the game files through steam. Though I would like to point out my score was in the negative, which lead me to believe it was a bug.
At the time I flew medium cargo just like others, but it happens with me sometimes with 737 passenger missions as well. It is always paired with two missed atc transmission, however I had a flight without missing any transmission, yet it still showed me this 2 missing atc transmission with the negative score. Now normally 2 missing transmission does not impact your score to the minus, so these might be something buggy transmissions. I did 60% airline procedure with flaps overspeed, landing without clearance and entering the taxiway, so the pilot performance generally doesn’t seem to impact it so wildly.
Flying for a while I noticed that there are atc transmissions that doesnt actually produce sound or dialogue in the comms, but it appears to press enter/interaction button to answer it, which I thought it could have gone unnoticed by me. But it might also be colliding atc transmissions that are blocked as another transmission / dialogue is taking precedent, and it seems like that there is a priority system which only allows one dialogue to play. I am unsure of the nature of it, but whenever this happens there is 2 missing atc transmissions amongst the pilot performance and to my perception, I didn’t miss any.