Yeah sorry this is kind of a documentation fail on our part.
You see, we fundamentally changed everything about media on the site.
It used to be that there were media galleries. Everything you uploaded was in the galleries, and either set to private or public. Problem was that this meant that it was impossible to move content around without making copies... things like news articles, contests, forum posts, NSTV etc. were all totally separate from the galleries.
When we created the new system we completely re-worked that entire concept. Now you can upload content directly to the site and not link it anywhere. This will be good especially when we finally overhaul media posting in forums. You can just dump content directly into a post and bam its up. No tagging, no publishing, nothing... just there. Then, if you decide later you want to publish it elsewhere, you can.
There's a lot of places you can publish your content now. Cults, contests, NSTV, NS Photo Galleries... and there's lots more that over time you'll be able to do. MyMedia is NOT your galleries, it is simply a repository of everything you have ever added to the site. If you tag it and publish it to a gallery, then it will show up. If you push it into an NSTV channel it will be there. But if you just leave it in MyMedia, then it is in a holding pattern and not published anywhere on the site. We called this state private, because we ended up having to remove the ability to publish to the gallery and keep it private. We may add this back in in the future.
So that is the important change with the desktop uploader. Even after its on the site and has encoded, its still sitting unpublished in MyMedia. You have to go publish it somewhere on the site to show up.
We are newschoolers. Expect us.