I am having this problem as well and have tried everything I found online and it is still not working. I have downloaded the version from your site dRachmad: WP-PrettyPhoto 1.6.2 when used in WordPress 3.1.1, and installed it.
I have my NGG Options/Effect/JavaScript Thumbnail effect set to "none" with the code fix as above: rel="wp-prettyPhoto[%GALLERY_NAME%]". Doesn't work- I also tried it set to "custom" with no luck.
I checked the source code of WordPress pages with prettyPhoto galleries that work, like tarbak.com, and my site's page with a test gallery inserted: janayeakel.com/NEW2011/gallery/ (site in progress!) and I have the prettyPhoto CSS & JS files showing in the source code- so not sure what the deal is.
I have tried so many galleries, (and so many fixes), and this one does just what I need, please help if you can. These are the other plugins I have installed at this time- before I try deactivating them, maybe you can tell me if one cause PrettyPhoto to not work:
Admin Menu Tree Page View Version 2.
Flexi Pages Widget Version 1.6.6
NextGEN Gallery Version 1.8.2
Quick Cache Version 110709
SI CAPTCHA Anti-Spam Version 2.7.3
Simple Section Navigation Widget Version 2.1
TinyMCE Advanced Version 3.4.2.1
WordPress Database Backup Version 2.2.3
Wordpress Page Widgets Version 1.1
Thanks so much for any help you can offer!! ~Jana