WP-Juicebox loads the 'juicebox.js' file in the web page only if it is required (if a Juicebox shortcode is discovered on the page).
However, for some reason, the 'juicebox.js' file is not being loaded in your web page.
I do not know why this might be but you can ensure that the 'juicebox.js' file is loaded into all your web pages by opening the 'wp-juicebox.php' file in a plain text editor and changing line 31 from:

add_action('the_posts', array(&$this, 'shortcode_check'));

... to:

add_action('wp_enqueue_scripts', array(&$this, 'add_scripts_wp_core'));

It looks like your problems may be due to your custom theme introducing whitespace in certain places.

Your theme inserts whitespace before the Gallery Id in the Juicebox shortcode which results in the search for a valid shortcode failing (which, in turn, results in the 'juicebox.js' file not being loaded).
For example, a Juicebox shortcode should look like this:

[juicebox gallery_id="1"]

... but yours looks like this:

[juicebox gallery_id=" 1"]

... (note the space before the '1').

Also, your theme inserts four blank lines at the top of your gallery's XML file which appear before the XML declaration resulting in the following error (which may be the reason for the "Config XML file not found" message being displayed).

WP-Juicebox cannot prevent against your theme adding whitespace.
(There are also four blank lines above the Doctype Declaration on your main page. These are likely to be coming from the same source.)

Check your theme's PHP files and make sure that there is no whitespace which might be output when the files are loaded. For example, you have blank lines at the top and bottom of your 'functions.php' file which are likely to be the cause of the XML file problem.

I'll try to clarify a couple of other issues from your post above.

WP-Juicebox galleries dare not structured like regular galleries are.
There are no gallery folders for galleries created by WP-Juicebox. All WP-Juicebox galleries share a common 'jbcore' folder (in the 'wp-content/plugins/wp-juicebox/' directory), the images are stored in the Media Library and the XML files for WP-Juicebox galleries are created dynamically when the galleries are displayed.

Juicebox itself comes with its own version of jQuery (bundled within the 'juicebox.js' JavaScript file) so there is no need to load a separate version of jQuery into your web page.
WP-Juicebox requires jQuery but it uses the version which comes bundled with WordPress, so again, there is no need to load a separate version of jQuery into your web page.

I've done some further testing and it looks like if you remove the two blank lines at the top of your 'functions.php' file and the two blank lines at the bottom of it, everything should be fine.
The whitespace should no longer appear at the top of your HTML or dynamically-generated XML pages or before the Gallery Ids in the Juicebox shortcodes.