5i25-7i77 upgrade to Linux 2.8.4 Debian

I have a perfectly fine working mill running on version 2.77 and I am trying to upgrade to 2.8.4 because I want to try probe_basic. I installed it, ran pnCConf, plugged the same PID numbers and expected it to work as the old one does.
To my great surprise it’s a total mess. All 3 servos appear to be completely out of tune. At first I thought I had made a mistake with the PID numbers but it’s not the case. Everything is correct. I don’t know what to think. Of course, I can go through the PID tuning process again and I know how to do it but it means I need to disconnect all the servos, etc.  I don’t understand why it would not work… All the hardware and even the computer are the same…

Check on both configs:
Servo period, should be 1 million.
Scaling, encoder, PID, FFn, should be the same.

I couldn’t find anything that would be any different from the original configuration. I ended up retuning the system.
Interestingly, I had to reduce the P by the factor of 10.
I and D and FFn are the same. It looks like the system is 10 times more “sensitive” to the P value. I cannot explain this.