Using a different theme and can't get shortcodes to work

I have changed the theme that I am using on my Opigno site and now I can not get shortcodes to work, specifically those that have animation like accordion, stats and skillbar. The theme I am using uses the Drupal Shortcode module, but that module is not compatible with Wysiwyg, which Opigno uses. I have disabled and unistalled shortcode module. I am able to turn shortcodes on for my text format and they partially work, but the jquery code for the animation appears as plain text on the page instead of the animation happening. Any hints would be appreciated. I'll keep digging.