IF I leave Artio Joomsef enabled all images for the zoo application pages are missing. As soon as I turn of Joomsef the images all re-appear with no issue.

I have looked at the FAQ, and the base path is correctly set in the htaccess file, so Im not entirely sure how to fix this.

Dear customer,

we are ready to help you. Please, send us a "Support Ticket" (www.artio.net/asupport/dashboard).
Also, please, state us more information. You can add some screenshots too.

Thank you and have a nice day!