When commenting on an activity post that had media uploaded via rtMedia the comments do not nest.
They appear to nest because of the ajax, but once you have created a few nested comments and refresh the page, they all become 1st level comments.
I have tested to see if the same error occurs with default BuddyPress functions and the comment nesting works fine.
The activity I commented on is here http://demo.rtcamp.com/rtmedia/members/demo/activity/10628/
Try and reply to any of the three first level comments then refresh the page.