I think I've got the same problem: if you have a shortcode that adds content to a page, Raptor will save the content back to the page and write over the shortcode.
For example, if you use the Testimonials Widget (TW) in amongst the content of a page using a shortcode, then edit something else on that page and save it via Raptor, the code generated by TW is also saved and "hard coded" into the content instead of the shortcode. This means that any further testimonials will be ignored by that page, and you have to go back into the regular WP editor to delete the "hard code" and replace it with the shortcode EVERY time.
This appears to be true of all shortcoded widgets when added to the content. Is there any way to get Raptor to avoid editing anything within [shortcode brackets]?