Seeing that my comment above has indeed helped someone to solve the problem I will post it as an answer.
The problem occurs if you switch from %matplotlib inline to %matplotlib notebook without restarting the kernel.
Switching from %matplotlib notebook to %matplotlib inline works fine.
So the solution is to either restart the kernel or start a new notebook.
It seems that in some cases it helps to repeat the setting of the notebook backend, i.e. call it twice like
%matplotlib notebook
%matplotlib notebook
An analysis for why that is can be found in this comment