Okay, not sure if this is a bug or a feature request...

It looks like the new code handles lightbox quite well. I was able to add rel="lightbox", and everything's pretty happy. However, lightbox uses []'s to specify a grouping, and that seems to mess things up.

So this works and displays an image:
[upload|file=splash.png|rel="lightbox"]

But this breaks and just shows the text:
[upload|file=splash.png|rel="lightbox[group1]"]

Here's the lightbox document I'm going off of:
http://drupal.org/node/276378