There is currently an inconsistency in the way that WordPress displays images in the media upload window which causes some confusion.

Try the following:
Create a new post, click the 'Add Media' button, drag and drop some images, select 'Uploaded to this post...' and note the order of the images. Close the media window and publish the post.
Now go back and edit the post, click the 'Add Media' button and select 'Uploaded to this post...' once again. You should notice that the order of the images is now reversed. Why this should happen, I do not know but it has lead to some confusion. (This is purely WordPress behavior and has nothing to do with the plugin.)

WP-Juicebox displays images in the initial order displayed by WordPress (immediately after they have been uploaded, before going back in to edit the post).
If you drag and drop images into a custom order, Juicebox will display the images in the reverse order displayed in the WordPress media window. With this knowledge in mind, you should be able to order your images as you wish. (They should never be displayed in random order unless you use Juicebox-Pro and set randomizeImages="TRUE".)

If you like, you can easily reverse the order in which WP-Juicebox displays images by opening the plugin's 'wp-juicebox/config.php' file in a plain text editor and changing the two instances of 'order'=>'DESC' (in lines 34 and 36) to 'order'=>'ASC'. The line numbers refer to the current version of WP-Juicebox (v1.3.2.0).