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              I was facing a similar issue (only 1 chart showing per page)
I figured the issue was that both the views were not getting unique ids and hence were not getting rendered.
I fixed the issue by changing line 316 of d3_views_plugin_style_d3.inc to
      'id' => 'view-d3-vis-' . $this->view->name . '-' . $this->view->current_display,
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