Steps to reproduce

1. Go to the question bank.
2. Create a question if there is not one there already.
3. Click the preview icon.

Note that the user menu appears in the pop-up, and it looks silly.

This pop-up uses $PAGE->set_pagelayout('popup');

While investigating this issue I suggest you also verify what goes on with the 'embedded', 'maintenance', 'print' and 'redirect' pagelayouts.