I have adapted the SimpleViewer SEO PHP Script for use with Juicebox galleries. (The code is entirely PHP and does not involve Flash at all.)
(1) Change the $imgpath variable to the absolute URL of your gallery folder.
(2) Paste the code into a file named 'juicebox-seo.php'.
(3) Copy the file to your gallery folder.
(4) In your gallery's embedding code, change:

<div id="juicebox-container"></div>

... to:

<div id="juicebox-container"><?php include("juicebox-seo.php"); ?></div>

(5) Make sure that the file extension for the web page containing your gallery's embedding code is '.php' rather than '.html'.

<?php
######################################################
# Project:      SimpleViewer SEO Gallery Plugin      #
# Version:      2.02                                 #
# Author:       Mikael Kjellstrom                    #
# License:      Copyright (c) 2010 Mikael Kjellstrom #
######################################################

######################################################
# Adapted for Juicebox by Steven Speirs, 2013        #
######################################################

$imgpath = 'http://www.yourdomain.com/pathtogallery/';  // The path to the gallery 
$altmaxchars = "50";   // The maximum characters of the TITLE and ALT tags taken from the title and caption 

$doc = new DOMDocument();
$doc->load( 'config.xml' );

$gallery = $doc->getElementsByTagName( "juiceboxgallery" );
foreach( $gallery as $gallery ) {
    $gallerytitle = $gallery->getAttribute('galleryTitle');
}

print "<div id=\"jbseo\">";
print "<h1>$gallerytitle</h1>";

$images = $doc->getElementsByTagName( "image" );

print "<ul>";

foreach( $images as $image ) {
    $largephoto = $image->getAttribute('imageURL');     
    $photo = $image->getAttribute('thumbURL'); 

    $titles = $image->getElementsByTagName( "title" );
    $title = $titles->item(0)->nodeValue;

    $alttitle = substr($title, 0, $altmaxchars);
    $pos = strrpos($alttitle, " ");
    if ($pos>0) {
        $alttitle = substr($alttitle, 0, $pos);
    }
    $title = htmlspecialchars($title);
    $alttitle = htmlspecialchars($alttitle);

    $captions = $image->getElementsByTagName( "caption" );
    $caption = $captions->item(0)->nodeValue;

    $altcaption = substr($caption, 0, $altmaxchars);
    $pos = strrpos($altcaption, " ");
    if ($pos>0) {
        $altcaption = substr($altcaption, 0, $pos);
    }
    $caption = htmlspecialchars($caption);
    $altcaption = htmlspecialchars($altcaption);

    print "<li style=\"list-style-type: none;\"><p><a href=\"$imgpath$largephoto\" target=\"_blank\"><img src=\"$imgpath$photo\" alt=\"$altcaption\" title=\"$alttitle\"/></a><br />$title<br />$caption</p></li>";
}

print "</ul>";

print "<p style=\"font-size: 10px;\">&copy; 2010 &middot; <a href=\"http://www.mkwebdesign.ca/tutorials/making-simpleviewer-seo-friendly/\" target=\"_blank\">Powered by SimpleViewer SEO Gallery Plugin</a></p>";
print "</div>"; 
?>

It looks like the combination of the following two configuration options is preventing caption links from functioning.

captionPosition="OVERLAY_IMAGE"
imageScaleMode="FILL"

I have logged a bug report and hopefully this will be fixed in the next version of Juicebox-Pro.
Thank you for reporting.

In the meantime, workarounds would be to use a different setting for either captionPosition or imageScaleMode .

The fact that browsers cache files is part of the functionality of the browsers themselves (rather than Juicebox-Pro).

If you wish to prevent browsers from caching your gallery's XML file (so that the current 'config.xml' file is always fetched from your web server), then try defining your gallery's XML file with a unique identifier (e.g. the current time which will be different each time the browser loads the page) using the configUrl option in your gallery's embedding code.

<!--START JUICEBOX EMBED-->
<script src="jbcore/juicebox.js"></script>
<script>
    new juicebox({
        containerId : 'juicebox-container',
        configUrl : 'config.xml?nocache=' + new Date().getTime()
    });
</script>
<div id="juicebox-container"></div>
<!--END JUICEBOX EMBED-->

You could then edit your gallery with JuiceboxBuilder-Pro and add your new images with new filenames (and remove any unwanted images) via the 'Images' tab.

You should no longer experience a caching problem.

As the image filenames form part of a URL when uploaded to a web server, it would be wise to use only web-safe characters.
Please see section 2.3 of this document for details: http://www.ietf.org/rfc/rfc3986.txt

JuiceboxBuilder-Pro should be able to handle all images whose filenames use any or all of these characters.

Could you perhaps zip and upload a couple of your photos (one whose caption is displayed and one whose caption is not) and provide a download link so that I can take a look at them and try to determine the cause of the problem? Thank you.

1. No. The Button Bar's position (set via the buttonBarPosition configuration option) can be set to OVERLAY, TOP or NONE and the its horizontal alignment (set via the buttonBarHAlign configuration option) can be set to LEFT, CENTER or RIGHT. The Button Bar configuration options can be found here.

2. Perhaps the font is included with Adobe AIR (and is displayed in the live preview window in JuiceboxBuilder-Pro) but is not installed on your computer. If you do have the font installed (viewers of your gallery would need to have it installed on their own computers in order to see it), then try the following code instead:

<style="font-family: futura;">Sahara Desert</style> 

@cqv

You can choose for JuiceboxBuilder-Pro to not process/resize your images by deselecting the 'Resize Images' checkbox on the 'Images' tab. JuiceboxBuilder-Pro will then simply copy your original images across to the output 'images' folder for use in the gallery.

No. The imageTransitionType configuration option is active in Large Screen Mode only (as noted in the options's description in the Main Images section of the 'Config Options' page).
In Small Screen Mode, the imageTransitionType is always set to the default value of 'SLIDE'.

Set showSplashPage="NEVER" in your gallery's XML file.
If creating or editing your gallery with JuiceboxBuilder-Pro, the 'Show Splash Page' configuration option can be found in the 'Customize -> Splash Page' section.

First of all, please try upgrading your Juicebox-Pro gallery from v1.1.1 to the current version (v1.2.0) by following the instructions here as many bugs have been fixed since v1.1.1. Please see the Juicebox - Version History for a full list of changes.

Also, try validating your web page with the W3C Markup Validation Service and fix the errors reported.
Once your web page validates correctly, it should be rendered with greater predictability and consistency across different browsers.

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 (www.mydomain.com is a subdomain of domain.com).
This is due to the JavaScript same-origin policy security restriction. Please see this web page for more information.

To have the gallery display when visiting both www.mydomain.com and domain.com, try using relative paths (rather than absolute paths which hardcode either www.mydomain.com or domain.com) in your embedding code.

You can set a gallery's dimensions to absolute pixel values (rather than percentages) with embedding code such as:

<!--START JUICEBOX EMBED-->
<script src="jbcore/juicebox.js"></script>
<script>
new juicebox({
containerId : "juicebox-container",
galleryWidth: "920",
galleryHeight: "920",
backgroundColor: "#222222"
});
</script>
<div id="juicebox-container"></div>
<!--END JUICEBOX EMBED-->

When doing so, your gallery will always be a fixed size, regardless of the size of the user's browser window.
If creating or editing your gallery with JuiceboxBuilder-Pro, you can set the gallery's dimensions in the 'Customize -> Lite' section.

When embedding your gallery with Adobe Muse (following the instructions here), you must set your gallery's height (to an absolute pixel value) in the gallery's own embedding code.
You can leave the gallery's width at 100% and then constrain the gallery to a fixed width using the width of the HTML frame in Adobe Muse.