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That's exactly right. You can actually get around our bad parsing by putting an extra empty line between \begin and \end. But then you will see another symptom of CSS issues, which should be fixed by #4159.
Closing as this issue is not in IPython itself and if still problematic and relevant should be opened on the right repository. This will allow to keep the number of opened issue on the IPython repo under control.
Feel free to keep commenting or reopen if necessary.
... or jquery code in triple backticks get mangled...
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