Thank you for your answer. I did double check my first channel measurments, because they seemed illogical to me also. So finally, the first channel seems perfectly right ( I did the measurments too late in the evening, and they were not good at all).
However, I can confirm the measurments on the second channel : everything seems right, except the TP7, TP9 and pin 1 of U16 which all have fixed, wrong values that never change.
I also checked, the connexion on the second channel doesn't affect the TP 12 and Tp 13 voltage from the channel 1 test steps 3 and 4 after I connect the channel 2. They are still ok ( about 2 % change in value when PCB B connected).