Hi there, I have experienced this same issue with several plugins, two being lightbox gallery plugins and one being a mapping plugin. I want to call shortcodes from within the template so that the end user does not have to worry about deleting or otherwise forgetting how to insert a particular item.
As an example, I can call the [gallery] shortcode fro within the template and it works almost perfectly. THe gallery displays correctly and is styled. The only error is that the shortcode only seems to activate any associated plugins when it is placed within $the_content, so the plugins remain unactivated when I call the shortcodes only using do_shortcode.
If I leave the d0_shortcode template tag in, but ALSO add the gallery shortcode in the content editor, then both galleries have the plugin effect applied,
so my question is, how can I make a shortcode called with do_shortcode still call the plugin.
nb the plugins this is happening on are
and several mapping plugins.