Yes. That is correct. Juicebox comes with its own version of jQuery bundled within the 'juicebox.js' file.
In doing so, we know that Juicebox will work.
Otherwise, we would have to rely on users including jQuery in their web pages (a further step in the embedding process) and we could not guarantee that the version of jQuery that the user uses does not have any bugs in it which would result in the Juicebox gallery failing to function correctly.

You might think that it would be OK to just use the the version of jQuery which comes bundled within the 'juicebox.js' file to save you from loading a separate version of jQuery in your web page.
However, if Juicebox ever changes its version of jQuery or strips out any jQuery functionality or changes its built-in JavaScript library completely, then your web page may break. Therefore, if your web page requires jQuery for anything other than Juicebox, I would recommend that you continue to load jQuery separately in your page.

No. There is no version of the 'juicebox.js' file available without jQuery included.

For other users reading this thread, in order to install a new version of JuiceboxBuilder-Pro, it is necessary to first uninstall any existing version.
Uninstall your existing JuiceboxBuilder-Pro version as follows:
Windows: Use the uninstaller in the 'Control Panel -> Programs -> Uninstall a program' list.
Mac: Delete the 'JuiceboxBuilder-Pro' file from the Applications folder and then empty your Trash afterwards.

If you have any version of JuiceboxBuilder-Pro on an external hard drive attached to your computer, please detach the drive before running the 'JuiceboxBuilder-Pro.air' installation file.

Also, please make sure that your version of Adobe AIR is also up-to-date.
The current version can be downloaded from here.

If this does not work, then in between uninstalling and reinstalling JuiceboxBuilder-Pro, try deleting the following folder manually:
Mac: /Users/your_username/Library/Application Support/Adobe/AIR/ELS/JuiceboxBuilder-Pro
Windows (XP): C:\Documents and Settings\your_username\Application Data\Adobe\AIR\ELS\JuiceboxBuilder-Pro
Windows (Vista, Win 7, Win 8): C:\Users\your_username\AppData\Roaming\Adobe\AIR\ELS\JuiceboxBuilder-Pro

I'm not sure what you mean by this. Could you please explain further?
Do you want the link to open in a new tab or window rather than in the same page?
If so, use the target="blank" attribute in your link, for example:

<a href="http://www.example.com/index.html" target="_blank">Link text goes here</a>

It is not possible to position a caption relative to the top of the main image.
However, you can set the height for a caption (depending on the value of captionPosition) with the maxCaptionHeight configuration options (in JuiceboxBuilder-Pro's 'Customize -> Caption' section).

If the caption is positioned on the overlay (captionPosition is set to either OVERLAY or OVERLAY_IMAGE), then you can control when the overlay is displayed with the showImageOverlay option (in JuiceboxBuilder-Pro's 'Customize -> Main Image' section) which can be set to AUTO (on hover), ALWAYS or NEVER.

Yes. For example, you could enter options such as the following into a gallery's Pro Options text area:

backButtonPosition="TOP"
backButtonUseIcon="TRUE"
backButtonUrl="http://www.example.com/index.html"

Please note that WP-Juicebox strips out any Lite Options which are entered into the Pro Options text area to avoid duplicate entries in the gallery's XML file. Lite Options can be set in the gallery settings window via the individual controls.

You can certainly change your WordPress theme and this will change the look and feel of your WordPress pages. However, no matter what theme you choose, your Juicebox galleries should remain constant (and can be modified in the gallery settings window).
If you want to see how a gallery looks when using certain configuration options, then try using JuiceboxBuilder-Pro on your computer. It supports all Pro Options via individual controls and has a live preview window which shows you how your gallery looks as you make changes. If you want to replicate a particular layout, then you can save the gallery (on JuiceboxBuilder-Pro's 'Publish' tab), open the gallery's XML file in a plain text editor, copy the configuration options and paste them into a WP-Juicebox gallery's Pro Options text area.

It would not be possible to implement a solution within WP-Juicebox (without re-writing the plugin) but you could do the following with a standalone gallery.

(1) Listen for a change in the user's browser window size using JavaScript.
(2) Determine the new width of the user's browser window.
(3) If a specified width threshold has been crossed, then reload the gallery setting the new configuration options in the embedding code.

For example, create a sample gallery with JuiceboxBuilder-Pro and replace the gallery's 'index.html' page with the following code:

<!DOCTYPE html>
<html lang="en">
    <head>
        <meta charset="utf-8" />
        <meta name="apple-mobile-web-app-capable" content="yes" />
        <style type="text/css">
            body {
                margin: 0px;
            }
        </style>
        <script type="text/javascript" src="jbcore/juicebox.js"></script>
        <script type="text/javascript">
            var a = '3', b = '3', c = 'LEFT', thresholdWidth = 600;
            function loadGallery(a, b, c) {
                new juicebox({
                    containerId: 'juicebox-container',
                    maxThumbColumns: a,
                    maxThumbRows: b,
                    thumbsPosition: c
                });
            }
            function thumbsStatus() {
                var windowWidth = window.innerWidth ? window.innerWidth : $(window).width();
                if (windowWidth < thresholdWidth && c === 'LEFT' ) {
                    a = '10';
                    b = '1';
                    c = 'BOTTOM';
                    loadGallery(a, b, c);
                }
                if (windowWidth >= thresholdWidth && c === 'BOTTOM') {
                    a = '3';
                    b = '3';
                    c = 'LEFT';
                    loadGallery(a, b, c);
                }
            }
            $(document).ready(function() {
                thumbsStatus();
                $(window).on('resize', thumbsStatus);
                loadGallery(a, b, c);
            });
        </script>
        <title>Test</title>
    </head>
    <body>
        <div id="juicebox-container"></div>
    </body>
</html>

Thank you for providing the URL to your gallery.

It look like the problem happens when captionPosition="BELOW_IMAGE" and the image is displayed fullsize (ie. when the browser window is large enough that the image does not need to be dynamically rescaled by Juicebox).
If you shrink your browser window so that the image is dynamically rescaled by Juicebox, then you should see the link become active.

I have logged a bug report with the developers and this should hopefully be fixed in the next version.
In the meantime, possible workarounds would be to try one of the following:
(1) Change the captionPosition.
(2) Change the imageScaleMode.
(3) Ensure that your images are large enough that they would need to be scaled down by Juicebox to fit within your gallery's image area.

If you set your gallery's height to a fixed pixel value (such as 600px), then it will be 600px in all devices and browsers.

You can change a Juicebox gallery's height in the gallery settings window.
By default, it is set to a fixed pixel value (600px) because setting a gallery's height to be a percentage (such as 100%) can cause problems if the gallery's parent container does not have a height set via CSS. Juicebox may then not be able to determine what its own height should be (100% of what?).

In a WordPress environment, you may have little control over the gallery's parent container which is generated by your theme. It is unlikely that a height will be set for the gallery's parent container as the theme has no way of knowing what content will be placed in the page or post and WordPress pages are designed to scroll vertically if necessary. (They are not intended to dynamically rescale vertically to fit within a user's browser window height).

You could try changing your gallery's height to a percentage but whether this works OK or not may be dependent on your theme.

I have been unable to replicate the problem you report in a test gallery of my own.
Please post the URL to your gallery so that I can take a look for myself. (There may be a combination of configuration options which is causing the problem.)

As you have not explicitly set a configUrl or baseUrl in your gallery's embedding code, Juicebox will, by default, look for your gallery's XML file to be named 'config.xml' and to be located in the same directory as the HTML page which contains the embedding code.
Therefore, your gallery's XML file should be located here: http://www.website-design.ca/exhibition/config.xml
... but it does not seem to be there. Going directly to this location in a browser results in an error 404 (file not found).

Upload your 'config.xml' file to your 'exhibition' directory and your gallery should display fine (as long as the paths within the XML file are correct).

If you want to rename or relocate your gallery's XML file, you can do so using the configUrl configuration option.
For example:

<!--START JUICEBOX EMBED-->
<script src="jbcore/juicebox.js"></script>
<script>
new juicebox({
configUrl: "/gallery/custom.xml",
containerId: "juicebox-container",
galleryWidth: "100%",
galleryHeight: "100%",
backgroundColor: "#222222"
});
</script>
<div id="juicebox-container"></div>
<!--END JUICEBOX EMBED-->

I'm glad you were able to get it working.
Thank you for sharing your code. Hopefully others will be able to benefit from it.

I have just viewed your gallery in Safari 5.1.7 on my PC (and two other browsers which use the WebKit engine: Chrome 33 and Opera 20) and I see no flickering in transitions.

As I do not see the flickering in your gallery when I view it myself, it looks like the problem may not be with the gallery itself or due to a code conflict but it seems to be localized to your own browser/system.
Try clearing your browser's cache before reloading your gallery to see if this makes a difference.

Do you see the flickering in any of these demo galleries?
http://www.juicebox.net/demos/

There are known issues (which are currently being investigated) whereby flickering can occur in Chrome if the gallery is either loaded into an iframe or hosted on Dropbox rather than on a regular web server.
However, your gallery is not hosted on Dropbox and is embedded directly in your web page.

I have viewed your gallery in Chrome 33 (and Firefox 28.0, IE11, Safari 5.1.7 and Opera 19.0) on my PC and do not see any flickering during image transitions at all in any browser.

Here are a few things to check and try:

(1) Try clearing your browser's cache before reloading your gallery's web page to see if this makes a difference.

(2) Try fixing the HTML errors on your web page.
You can check the code on your web page with the W3C Markup Validation Service and then fix the errors that are reported.
(There is a closing </p> tag on your web page with no matching opening <p> tag.)

(3) Try viewing your gallery on its own web page (rather than embedded in your main web page) to see if the flickering still occurs (to see if there is perhaps a conflict with some CSS or JavaScript code on your main web page): http://www.paradiseblue.com/gallery1/

If none of the above helps , then please post back and let me know what operating system and version number do you use. It might give us a clue to the source of the problem.