I contacted the theme creator and got this reply.
“I understand the plugin indexes the shortcode content. It sounds like it’s trying to run the shortcode PHP file without fully executing the theme so a required file is probably missing since it wasn’t loaded. If you can disable the shortcode indexing please try that first. You’ll have to contact the plugin author for more details about how it achieves the indexing because I have no idea how that plugin functions.”
I disabled that option and it now works so that was the problem. Could this be fixed? I have to say this search is fantastic. I’ll be buying the pro version for sure. Thing is two important parts of my site are both loaded via short codes. So it would be much better if I could get them indexed somehow.