I am running Wordpres 3.6 (newest) and updated NextGen to version 2.0.7 from the previous version that broke many sites themes (sorry, I didn't catch the previous version number... probably 2.0.6?). The new update to version 2.0.7 did fix my themes issues (a child theme of the official 2011 theme).
I used infinite-scroll (http://wordpress.org/plugins/infinite-scroll/) on a website http://www.amsat.org I help with and the update in fact stopped the infinite scroll functionality. When NextGen was deactivated the functionality returned. This was performed on a development server but I would like to let you know about the issue so it may possibly be addressed.
Please let me know if you need anything else to help fix this issue with NextGen and Infinit-Scroll.