[Plugin: WP Gallery Custom Links] installed not working: missing something?

This was resolved over email, but for posterity, the Flashlight theme had a couple different custom gallery layout options, including a 3-column layout and a “WordPress default gallery” option. The 3-column option used a function built into the theme to draw out the gallery, and didn’t use the [gallery] shortcode at all. The “WordPress default gallery” layout option did use the [gallery] shortcode, but instead of saving the gallery images as page attachments, the theme was creating its own custom “gallery-images-for-ID” post, and the uploaded images were attached to *that* post instead of the page being edited.

So because the page technically had no attached images (which is what the WP Gallery Custom Links plugin looks for to do URL replacement) and the theme used a customized method for saving uploaded gallery images (not as direct page attachments), it is beyond the scope of what the plugin was designed to do. Either the theme would need to be customized in order to support the plugin, or the plugin customized to support this particular theme.