In the previous version of WordPress I was able to re-order the slideshow by going to the media uploader and dragging/dropping the images to the correct order. Then I would "save changes" and the new order would be reflected in the slideshow.
It seems like with 3.5 changing the order has no effect.
The new code WordPress generates is [gallery ids="466,474,468,469,467,470,471,472,473"] so I am assuming the order is now created here, vs. behind the scenes in the media uploader.
Is there any way to add these string of ids to the [portfolio_slideshow]? Or a way to change the order of the images?