The plugin is working great on my production site, but I’ve broken something on the root site of my test server.

I can create new shortcodes – no problem

When I *edit* existing shortcodes, they save as a Post (i.e. no longer a shortcode content type)

I have deleted and re-installed the plugin, am on WP 3.9, and when I activated on a sub-site of the same server, it works fine. <s>May be a conflict with another plug in - the main suspect </s>
Never mind, found it is Post Type Switcher – will report it there…
So this is just an FYI – just in case you might be able to get your plug in to play nice with theirs….?

https://wordpress.org/plugins/shortcodes-ui/