Yeah, I have a similar issue.
I’m trying to generate the shortcode myself a plugin and some javascript. The shortcode gets generated just fine; I can print it to the webpage and insert the very same shortcode on a different page and it displays. And the generated shortcode, when passed to the do_shortcode() function does insert the markup on the page, but for some reason, the chart does not display.
I’m not sure if there’s something else I need to do (like a repaint, or redraw, or something) but I can’t find anything useful online to assist in this issue. :/
Would be nice if we could get some responses on these topics from the plugin authors.