As we all are familiar, the NextGEN slideshow doesn't work correctly when using AAPL. I spent some time looking into the code, and it really comes down to this snippet of HTML from the actual page:
NextGEN outputs this snippet for each shortcode found within the page/post. That goes for the script block as well. Then the deferred script relies on the document being ready. Well, the page is only ready once. The subsequent AJAX calls do not result in this event being fired again. Also, you can't re-fire the ready event.
The solution may come down to using jQuery to hunt down the code, and try and figure out a way to call the code in the ready event callback. Ideas?