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The problem you're describing is actually intentional behaviour. It's been raised before in separate issues (#60 and #4). On the first call, matplotlib recognises that there doesn't exist a figure object, so it creates one. On the second call, despite not being shown, the figure still exists, so plot() adds to that figure, but also doesn't return any output.
The reason for this problem is that we currently don't communicate back to python that when the cell output is overwritten, the figure should be closed (this is hard).
There are good reasons for this, since one sometimes wants to create figure, but show it later.
What I do:
%matplotlib
The only thing that fixes the problem is kernel restart
Here's a video recording https://cloudup.com/c5e24HCaLI6
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