I’m experiencing the same issue with the sidebar widget display.
Re the template tag: To get the template tag to display the table of contents it needs to be inserted after the_content() has been executed.
The plugin does not output correct html. Lots of extra unclosed ul or ol and an extra </div>
If I insert the template tag into by sidebar (not using the widget or a text widget) it works fine.
Format of widget fixed (removed all orphan /li, there arent unclosed ul). Widget is code clean now (in version 1.5.6)