Hello everyone ,
I updated to version 4100 and since I see a fault in the GPIOs of the raspberry:
I am using a raspberry GPIO to pulse to an external hardware watchdog.
the pulse is managed directly by raspbian:

import RPi.GPIO as GPIO
import time
PULWD = 16 # BCM / GPIO
GPIO.setwarnings (False)

GPIO.setmode (GPIO.BCM)
GPIO.setup (PULWD, GPIO.OUT)

while True:
GPIO.output (PULWD, 0)
time.sleep (0.5)
GPIO.output (PULWD, 1)
time.sleep (0.5)

so far this has always worked with all other versions of codesys.
since the update, as soon as my codesys program is in RUN on the raspberry, the GPIO signal is completely random.
when the program is in STOP, the GPIO signal flashes again normally ....
I am not using any raspberry GPIO in the codesys program.

Thanks for your help.

Hello everyone,
if it helps:
not using GPIOs_A_B, I disabled it in the program and that solved my problem.
although GPIOs appear as "not used", it seems that this is not taken into account well in codesys.

this remains a problem for those who want to use GPIOs_A_B

Thanks a lot for this report, and even tracking down the problem this far. I appreciate this!

which Raspberry Pi Model do you use? For anything newer than the Pi B, meaning Pi2, pi3, pi4 or PiB+, you should be using the other device description. (Right click the gpio, update device, select the device description "GPIOs B+/Pi2")

Hi,
You're welcome ingo, it seems to me that's the purpose of this forum, some helped me when I was stuck, so if I can save others from spending hours looking for solutions.
it would be nice if codesys looked at the problem too....
otherwise, I use a raspberry pi4, and the device is updated on "GPIOs B + / Pi2" as in the picture.