After adding the images to your gallery in the media upload window, I expect that you are probably clicking the 'Insert into post' or 'Create a new gallery' button. This will display the images directly within your WordPress page or post (in addition to attaching the images to the page or post, which is all that is required to add the images to your Juicebox gallery).
(Incidentally, the 'Create a new gallery' button refers to a WordPress gallery and this is unconnected to WP-Juicebox.)
The key is to simply close the media window (via the cross in the top right corner) after the images have finished uploading.
(This is noted in the 'Adding Images From WordPress Media Library' section in the WP-Juicebox support page.)
As soon as the images have finished uploading, they will be attached to the page or post and will be displayed in your Juicebox gallery.
I hope this helps.