Currently the Atom feed parse method in FeedsYoutubeParser.inc looks for the video ID in the yt:videoid tag. However, that tag isn't present in the API 2.1 uploads and favorites feeds I've tested, e.g. http://gdata.youtube.com/feeds/api/users/Novumsquare/uploads. On import, this results in a video URL without an ID, and multiple nodes not being created if the replace option is selected and video URL is the unique target in the node processor (because all have the same http://www.youtube.com/watch?v= URL).

The entry ID tag contains a URL with the video ID. I'd suggest using a similar approach to the RSS method, i.e. replace

$id = (string) $yt->videoid;

with

$id = end(explode('/', $entry->id));

Or if yt:videoid is still present in some feeds, use the line above as a fallback.