This would be a CSS rule that is applied to all instances of a particular HTML element, such as a div.
For example, something like:

div {
    display: none;
}

... will apply to all divs on your web page (including those in your Juicebox gallery), whereas:

#sample {
    display: none;
}

... will apply only to the div with id="sample".
It sounds like your theme may be the root of the probem. Please let me know whet theme you used so that I can investigate further.

Your gallery currently used the following code:

backgroundColor: '#222222'

Change this to:

backgroundColor: 'rgba(0,0,0,0)'

The 4th parameter of the rgba expression (the alpha channel) is the opacity of the background (0 being transparent and 1 being opaque). If you use a 6-digit hexadecimal code rather than an rgba expression, the gallery's background will be opaque.
If using JuiceboxBuilder-Lite to create or edit your gallery, set the opacity of your gallery's background color to 0 on the 'Customize' tab.

The gallery's own 'index.html' file is used only to display the gallery on its own page (for example if linking directly to the gallery of embedding it in an iframe).
If you are embedding the gallery in an existing HTML page alongside other content, then the gallery's own 'index.html' file is not required and you do not need to upload it to your web server.
Therefore any Google search result (we are currently investigating integrating SEO techniques into Juicbeox-Pro) will point to your own web page (and cannot possibly point towards the gallery's own 'index.html' page because it does not exist on the internet).

If you have a Flickr Pro account, you could set flickrImageSize="ORIGINAL" to pull your original images from Flickr into your Juicebox-Pro gallery.
Please see the description of the flickrImageSize configuration option in the Flickr Pro Options section of the Config Options page for more information.

Audio Options should work fine on an iPad.
Try viewing the demo gallery here and click the 'Toggle Audio' button on your iPad.
Check that your own gallery's audio URLs are correct and if you continue to experience problems, please post the URL to your gallery so that I can take a look.

Edit:
Thank you for providing the URL to your gallery via email.
I have taken a look at your gallery and it uses playAudioOnLoad="TRUE".
As documented in the description for this configuration option in Audio Options section, this option is not supported on iOS.

If you would like users to be able to hear your audio track on iOS devices, you would need to set showAudioButton="TRUE" and allow users to click the Audio Button to start the track playing.

Also, I notice that your gallery sets only audioUrlMp3. For better support across all browsers, you could also set an OGG audio track using the audioUrlOgg configuration option.
(Firefox does not have native support for MP3 files but does support OGG files.)
Please see the Adding Audio section for further details.

This <meta> 'viewport' tag has been removed in the latest version of WP-Juicebox (v1.2.0.1) which can now be downloaded from this web page.

This is not possible in a Juicebox-Pro gallery. All thumbnails are the same size and the dimensions are determined by the thumbWidth and thumbHeight configuration options.

At first, I thought the problem may have been caused by a timing issue.
However, on further investigation, I have tracked down two bugs which are causing the problems you are experiencing.
The problem with the caption showing stems from setting screenMode="SMALL" and having the cursor hover over the thumbnails as the gallery displays (which happens regularly in your scenario as the links to your galleries are in the same position in your web page as the thumbnails in your galleries).
The problem with the thumbnails not being responsive stems from the additional setting maxCaptionHeight="700".
I have logged bug reports and hopefully they will be fixed in the next version of Juicebox-Pro.
In the meantime, the only sure solution would be to not set screenMode="SMALL".

@ijordache

Try replacing the following line in your 'makeup.html' page:

<div id="dropmenu1_a" class="dropmenudiv_a">

... with:

<div id="dropmenu1_a" class="dropmenudiv_a" style="z-index: 999;">

@krissymac

I have not been able to determine the exact problem in your gallery but feel fairly sure that it can be resolved with appropriate 'z-index' values. Your menu should appear on top of your gallery if you:
(1) Remove all existing 'z-index' entries from your 'style.css' file.
(2) Change line 49 of your index.html page from:

<div class="container_12">

... to:

<div class="container_12" style="z-index: 999;">

Thank you for letting me know what operating system you use.
I have notified the developers of this issue (missing thumbnails in the JuiceboxBuilder-Pro 'Images' tab) and hopefully it will be fixed in the next version of Juicebox-Pro.
In the meantime, please try Adobe AIR 3.3 and, hopefully, you will be able to see all your thumbnails within JuiceboxBuilder-Pro.

I have now fixed the link in my previous post.
Apologies for any inconvenience caused.

This code is only suitable for those who wish to embed their galleries in iframes and do not wish to allow their galleries to be viewed on pages of their own. This is likely to be a small subset of all users and we recommend using embedding code in preference to iframes as embedding a gallery in an iframe will limit its functionality (the 'Expand Gallery' button is disabled and the 'Back Button' will not work).
It is easy enough to copy and paste this code where necessary but we do not want to encourage users to do something (use an iframe) which will limit the functionality of the gallery.

The embedding code provided on the 'Publish' tab of JuiceboxBuilder-Lite works fine when following the embedding instructions here.

www.xtreme-remodeling.com is a subdomain of xtreme-remodeling.com and all your gallery files must be on the same domain or subdomain due to the JavaScript same origin policy. Please see this web page for further details.

Your gallery currently uses the following code:

<script src="http://www.xtreme-remodeling.com/dream-deck-gallery/jbcore/juicebox.js"></script>

... so the gallery will display only when you access it using http://www.xtreme-remodeling.com/dream-decks.htm (and not http://xtreme-remodeling.com/dream-decks.htm).

Use relative paths within your embedding code and your gallery should display at both www.xtreme-remodeling.com and xtreme-remodeling.com

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

If your gallery's XML file is named 'config.xml' (which it is by default when creating a gallery with JuiceboxBuilder-Lite) and is located in the same directory as the HTML page continaing the embedding code, then there is no need to use the configUrl configuration option. (You will need to specify a configUrl only if you rename or move your gallery's XML file.

The code can be tweaked in any number of ways. Whether or not removing the <img> tags from your code will harm your SEO results, only time will tell.