Juicebox uses a Flickr API search to fetch the required images from Flickr's servers. The API search terms will be the same each time so if the results are inconsistent, this may be due to a problem at Flickr's end.
Please post the URL to your gallery so that I can take a look and see if I can replicate the problem you are experiencing.

From what you have said, it sounds like your pop-up is still classed as being your main overview page and, as such, blocking the shortcode from running on one will also block it from running on the other. There may be no easy solution. However, please check your email. I have sent you a message with an email address where you can provide me with your web server and WordPress login details if you like.

My suggestion to embed the gallery in an <iframe> is an alternative to using the WP-Juicebox plugin. It is not possible to use WP-Juicebox in conjunction with the <iframe> embedding method.

Please see this FAQ regarding the "Juicebox Error: Config XML file not found" message.
When I view my gallery I see the message 'Config XML file not found'. How do I fix this?

When embedding a gallery into an <iframe>, here are a few pointers:

• Make your gallery's dimensions 100% x 100% (so that it fills the <iframe> no matter what its dimensions are).

• Once you have created your gallery with JuiceboxBuilder-Pro, do not modify the embedding code in the 'index.html' file and do not move or rename any files within the gallery folder.

• Upload the complete gallery folder (not just the contents) to your web server.

• Use an <iframe> such as the following, ensuring that the 'src' attribute of the <iframe> points towards the 'index.html' page inside the gallery folder.

<iframe src="http://www.example.com/gallery/index.html" width="800" height="600" frameborder="0" scrolling="no"></iframe>

The issue could be caused by the CSS of your current WordPress theme clashing with the CSS of the Juicebox gallery itself.
You could try temporarily changing your WordPress theme (perhaps to the default Twenty Ten theme) to see if this resolves the issue.
If is does, you could then try isolating the Juicebox gallery from the rest of your web page (to avoid such CSS clashes) by embedding the gallery using an <iframe> instead of the embedding code currently used by the WP-Juicbebox plugin. This method of embedding is documented as Option #2 here.

It would involve the following steps:
(1) Create the Juicebox gallery on your computer using a program such as JuiceboxBuilder-Pro.
(2) Upload the entire gallery folder to your web server via FTP.
(3) Embed the gallery in a WordPress post using an <iframe> such as the following, ensuring that the 'src' attribute of the <iframe> points towards the 'index.html' page inside the gallery folder. Also, make sure that, when entering the <iframe> code into the body of your post, the method of entry is 'HTML' rather than 'Visual'.

<iframe src="http://www.example.com/gallery/index.html" width="800" height="600" frameborder="0" scrolling="no"></iframe>

Your gallery is located at http://www.fabianbond.co.uk/ but the link from the Google search directs the user to http://fabianbond.co.uk/ (i.e. not the 'www' subdomain where the gallery is located).
In order for a Juicebox gallery to function correctly, all the files (including the HTML document containing the JavaScript embedding code) must be on the same domain or subdomain.
This is due to the JavaScript same-origin policy security restriction. Please see this web page for more information.
Try changing the URLs in your gallery's embedding code from absolute URLs using the 'www' subdomain to relative URLs.
For example, change:

<!--START JUICEBOX EMBED-->
<script src="http://www.fabianbond.co.uk/FabianBond/Country/jbcore/juicebox.js"></script>
<script>
  new juicebox({
      containerId : 'juicebox-container',
      baseUrl : 'http://www.fabianbond.co.uk/fabianbond/Country',
  });
  </script>
<div id="juicebox-container"></div>
<!--END JUICEBOX EMBED-->

... to:

<!--START JUICEBOX EMBED-->
<script src="../Country/jbcore/juicebox.js"></script>
<script>
  new juicebox({
      containerId : 'juicebox-container',
      baseUrl : '../Country',
  });
  </script>
<div id="juicebox-container"></div>
<!--END JUICEBOX EMBED-->

Otherwise, you would need to either:

• Ensure that the Google search result points to http://www.fabianbond.co.uk/, or...

• Redirect/forward http://fabianbond.co.uk/ to http://www.fabianbond.co.uk/ without masking the domain name, or...

• Embed your gallery using an <iframe> instead of the JavaScript embedding code (documented as Option #2 here).

No matter where WordPress displays a post containing a Juicebox gallery (whether it is on an overview page along with other posts or on a page of its own), the shortcode within the post (e.g. [juicebox gallery_id="4"]) will be processed and the gallery will be displayed.
You can override this behavior by modifying the plugin's 'wp-juicebox.php' file. Open 'wp-juicebox.php' in a plain text editor and replace the shortcode_handler() function (lines 1052 - 1106 inclusive) with the following:

    function shortcode_handler($atts) {
        extract(shortcode_atts(array('gallery_id'=>'0'), $atts));
        if (is_singular()) {
            if ($gallery_id != 0) {

                $gallery_filename = $this->get_gallery_path() . $gallery_id . '.xml';

                if (file_exists($gallery_filename)) {

                    $dom_doc = new DOMDocument();
                    $dom_doc->load($gallery_filename);

                    $settings_tags = $dom_doc->getElementsByTagName('juiceboxgallery');
                    $settings_tag = $settings_tags->item(0);

                    $gallery_width = $settings_tag->getAttribute('e_galleryWidth');
                    $gallery_height = $settings_tag->getAttribute('e_galleryHeight');
                    $background_color = $settings_tag->getAttribute('e_backgroundColor');
                    $background_opacity = $settings_tag->getAttribute('e_backgroundOpacity');
                    $background_rgba = $this->get_rgba($background_color, $background_opacity);

                    if ($gallery_width == '') {
                        $gallery_width = '100%';
                    }

                    if ($gallery_height == '') {
                        $gallery_height = '600px';
                    }

                    $upload_dir = wp_upload_dir();
                    $gallery_filename = $upload_dir['baseurl'] . '/juicebox/' . $gallery_id . '.xml';

return <<<EOF
<!--START JUICEBOX EMBED.-->
<script type="text/javascript">
    new juicebox({
        backgroundColor : '$background_rgba',
        containerId : 'juicebox-container$gallery_id',
        configUrl : '$gallery_filename',
        galleryHeight : '$gallery_height',
        galleryWidth : '$gallery_width'
    });
</script>
<div id="juicebox-container$gallery_id"></div>
<!--END JUICEBOX EMBED.-->
EOF;

                } else {
                    return '<div><p>WP-Juicebox Gallery Id ' . $gallery_id . ' has been deleted.</p></div>';
                }
            } else {
                return '<div><p>WP-Juicebox Gallery Id cannot be found.</p></div>';
            }
        } else {
            return '<div><p>Open post to view WP-Juicebox Gallery Id ' . $gallery_id . '.</p></div>';
        }
    }
}

Save the file and re-upload it to its original location ('wp-content/plugins/wp-juicebox/wp-juicebox.php') overwriting the original file.

Thank you for reporting.
This is a known issue which has been addressed and will be fixed in the next version.

Your web page does not have a Doctype Declaration.
Please see this FAQ for details:
My gallery looks strange in Internet Explorer 9. Why?

That is correct. This is a limitation or WordPress itself, not WP-Juicebox.

Installing and using the Shiba Media Library plugin should not conflict with WP-Juicebox. (If you find any conflicts, please post back to let me know.)

As WordPress natively supports attaching a Media Library image to only one page or post, it can list only one page or post in the 'Attached to' column. As the Shiba Media Library plugin is responsible for attaching an image to multiple posts, I would expect the plugin to also be able to keep track of the posts and list them but I do not know if this is the case.

Yes. Attach a Media Library image to the post containing the gallery (from within the Media Library itself) and then either:
(1) 'Edit' and 'Update' the post containing the gallery
... or:
(2) Go to the 'WP-Juicebox -> Manage Galleries' page and 'Edit' and 'Save' the gallery (without changing any settings)
Either of the above will rebuild the gallery's XML file (which is necessary to include any new images).

Thank you for reporting. I have logged a bug report.

Not as far as I am aware. You would currently have to integrate such functionality manually.
These two forum threads may be useful to you:
http://juicebox.net/forum/viewtopic.php?id=148
http://juicebox.net/forum/viewtopic.php?id=160
Please post feature requests in this forum thread. It keeps them all together and ensures that they are not overlooked. Thank you.

The caption area does appear but is completely transparent and the captions, being white, do not show up well against your web page's background.
At first sight, it looked like there may have been a CSS clash between that of your web page and the gallery itself.
However, I have created a test gallery using the same HTML code and XML settings as your gallery does and loading the same external CSS and JavaScript files that your web page does but I have been unable to replicate the problem you experience in IE8.
Try re-uploading your gallery's 'jbcore' folder to ensure that all core files are present and correct.
Also, try setting captionBackColor="rgba(0,0,0,.5)" in your gallery's XML file.