Well I can’t say I know what might be going wrong.
Things you can try:
Use a new location for the button on the MC not overwriting an old one.
Make sure it is a key command and not a Eucon command you are putting on the jog wheel.
Check Nuendo’s key commands for what the new jog wheel function is doing wrong, for example, you said it was turning sync on and off. Check to see what key command that is in Nuendo, maybe remove those key commands, or change them.
I can’t say I have ever had this problem, so I don’t know what else to suggest.
I am open the rest of the day here, so I may do a quick video to show it.