If you do not set playAudioOnLoad="TRUE" or showAudioButton="TRUE" (to allow audio functionality), then audioUrlMp3 will not actually be used and its entry in the gallery's 'config.xml' file will just be redundant.
If you wanted to prevent audioUrlMp3 from being written to the gallery's 'config.xml' file, then you could change line 42 of the plugin's 'config.xml' file from:

if (value ~= tostring(model.default[key])) then

... to:

if (value ~= tostring(model.default[key]) and key ~= "audioUrlMp3") then

Thank you for the additional information.
I now see the problem in your sidebar gallery when the menu is not fixed to the top of the page.

It looks like it might be enough to just add the following to your web page's CSS:

.collapse {
    z-index: 9999;
}

Add this to the existing .collapse code in your 'bootstrap.min.css' file (on line 2704) and it will be included in all of your web pages that load the CSS file.

Hopefully this will solve your problem.

For reference, further information about UberMenu and 'z-index' issues can be found here.

I see the problem now in a large desktop monitor. (I was previously using my laptop.)
The problem is seen only when there is space between the main image and the thumbnails (which is why you see the problem only in expanded mode and I did not see the problem on my laptop).

The problem seems to be due to setting imageTransitionType="CROSS_FADE" and it is not directly related to the AutoPlay functionality.
If you are currently viewing the last thumbnail on a thumbnail page and manually navigate to the next image using the main image navigation button, the problem can be seen.

I have logged a bug report with the developers and this should hopefully be fixed in the next version of Juicebox-Pro.

In the meantime, possible workarounds would be to either:
(1) Set imageTransitionType to SLIDE, FADE or NONE.
... or:
(2) Make your gallery images larger so that, even on large monitors or in expanded mode, the images fill the image area from top to bottom (so that the problem cannot be seen).

I am unable to see the problem when viewing your gallery in Chrome, Firefox or IE11 on my PC.
What browser (or browsers) to you see the problem in?
Also, does the problem happen only in expanded mode or also in normal mode?

I notice that your gallery uses Juicebox-Pro v1.4.4 which was released only a week ago.
Try completely clearing your browser's cache before reloading your gallery's web page to make sure that your browser is not using cached files from previous versions of Juicebox-Pro.

The problem is likely to be due to the backslashes in your gallery's imageURL and thumbURL paths (in the 'config.xml' file). As these are relative paths, use slashes instead.
For example, change:

imageURL="images\0000029709.jpg"

... to:

imageURL="images/0000029709.jpg"

A couple of other things to check/try...

In your gallery's embedding code (in the 'index.html' page), change:

useThumbDots: "0"

... to:

useThumbDots: "TRUE"

This will probably not make a difference but possible values for the useThumbDots configuration option are TRUE and FALSE (rather than 1 and 0).

Also, try removing the comment from the top of the 'config.xml' file.

Hopefully this will solve your problem.

The image data must be in the required <image> tag format (using imageURL and thumbURL attributes) in an XML file.
It is not possible to provide the image data to Juicebox via JavaScript in the embedding page.
Please see Step #4 ('Edit config.xml') in the Manually Creating a Gallery support section for a sample <image> tag.
You could, however, use a server-side scripting language (such as PHP) to extract data from a custom source and build the XML file dynamically (see the example in my first post above).

The bug noted above (whereby a page containing an embedded gallery cannot be scrolled in Windows mobile devices) has now been fixed in Juicebox v1.4.4.
Please see the Upgrading Juicebox support page for instructions on how to download the latest version and upgrade existing galleries.
Please see the Version History for a list of changes between versions.

You're welcome!
I'm glad I was able to help.

The bug noted above whereby the default value of maxThumbRows (1) is not respected on small screen devices when screenMode="LARGE" has now been fixed in Juicebox v1.4.4.
Please see the Upgrading Juicebox support page for instructions on how to download the latest version and upgrade existing galleries.
Please see the Version History for a list of changes between versions.

If your thumbnails are not displaying locally or on your web server, then please double-check that the thumbnail images exist in the 'thumbs' folder and that the thumbUrl entries in your gallery's 'config.xml' file exactly match the thumbnail filenames taking care with case-sensitivity, especially with file extensions. For example, on a case-sensitive web server, 'image.jpg' is not the same as 'image.JPG'.

The link you provided seems to be an incomplete URL. I get an error 404 (file not found) when opening the URL in a browser.

If you like, please zip the entire gallery folder that is causing you the problem, upload it somewhere (perhaps your web server or a file sharing service such as Dropbox or Google Drive) and post a download link.
If I am able to see the complete gallery (rather than trying to find individual files on your web server, not knowing what all the actual filenames of your images may be), I should hopefully have a better chance of figuring out the cause of your problem. Thank you.

@juicebuck

Please post the URL to your gallery's web page so that I can take a look at the problem for myself and hopefully help.

Juicebox was designed to be embedded into a <div> in a web page.
Do you have an example of the issue you are having? If so, please post the URL to your page so that I can take a look and hopefully help further. Maybe if I see your gallery in your page, I will have a better understanding of your problem.
Thank you.