It looks like you might have already solved your problem.
When I go to your web page, your gallery displays and functions correctly.
If you do not see the gallery in your web page, then try clearing your browser's cache before reloading your web page to see if this makes a difference.

Try using relative paths for your baseURL and configURL (rather than absolute paths which hardcode your 'www' subdomain) so that your web site displays correctly on both http://comingsoon.it and http://www.comingsoon.it.
Also, when using a baseURL, as long as your gallery's XML file is named 'config.xml' and is located in your gallery folder, then you do not need to use a configURL to point to the XML file.

Try changing:

baseUrl : 'http://www.comingsoon.it/testArea/anteprime/emma/',
configUrl : 'http://www.comingsoon.it/testArea/anteprime/emma/config.xml',

... to either:

baseUrl : '/testArea/anteprime/emma/',

... or:

baseUrl : '/imgdb/primopiano/impaginate/emma/',

... as you seem to have uploaded your gallery folder to two different locations on your web server.

All of your web pages seem to use different code (with different CSS) which accounts for the change in position of your menu across your different web pages.
Also, some pages load your 'style-menu2.css' file whereas others load your 'style-menu4.css' file.
The 'style-menu4.css' file includes the following CSS rules (not found in the 'style-menu2.css' file) which will affect the position of your menu only on web pages which load this file.

#menu_left{
margin-left:20%;
}

#entete_left{
margin-top:7%;
margin-left:16%;
}

Try to use a single web page as a template and change only the content to create new pages.
Also, use the same CSS code for each and every page and the results will be consistent across all your web pages.

That is correct. The thumbnails were designed more as a navigational tool. As long as you set imageScaleMode to either SCALE_DOWN (the default value) or SCALE, your main images will be displayed in their entirety within the gallery's image area with their aspect ratios respected and without any cropping.

You can use the languageList configuration option to translate the word 'of' (the last entry in the languageList) to something else, such as 'des' or '/'. Please see here for details.
For example, you could use the following to display "1 / 3", "2 / 3", etc.

languageList="Show Thumbnails|Hide Thumbnails|Expand Gallery|Close Gallery|Open Image in New Window|Images|View Gallery|Next Image|Previous Image|Play Audio|Pause Audio|Show Information|Hide Information|Start AutoPlay|Stop AutoPlay|AutoPlay ON|AutoPlay OFF|Go Back|Buy this Image|Share on Facebook|Share on Twitter|Share on Google+|Share on Pinterest|Share on Tumblr|/"

(Alternatively, you could hide the paging text completely by setting showPagingText="FALSE" and showSmallPagingText="FALSE".)

Yes. With Juicebox-Pro, you can set the dimensions for your gallery's thumbnails using the thumbWidth and thumbHeight configuration options. All thumbnails in a Juicebox-Pro gallery will be the same size as each other but they do not need to be square.
If you create your gallery with JuiceboxBuilder-Pro, the application will create thumbnails at the specified dimensions and will set the appropriate values for thumbWidth and thumbHeight in the gallerys 'config.xml' file.

For reference, a list of all Juicebox-Pro Thumbnail Options can be found here.

If you are not able to upload .mp3 or .ogg files to your web server then you will need to host the files elsewhere (either another web server or perhaps a Dropbox public folder) and refer to them in the audioUrlMp3 and audioUrlOgg configuration options using absolute paths such as the following:

audioUrlMP3="https://dl.dropboxusercontent.com/u/134593202/music.mp3"
audioUrlOgg="https://dl.dropboxusercontent.com/u/134593202/music.ogg"

So, have you identified an error in this line of code, or is it a temporary fix unique to my case?

The code within the Drupal module should work OK (it is valid PHP and should work according to the PHP specifications) so I suspect a bug in your web server's PHP version (v5.3.26) may be the cause of the problem.
I have a feeling that if your web server's version of PHP was upgraded (to a version where this bug has been fixed), then there would be no need to apply this fix.

You could check the width of the user's browser window using JavaScript and then set the showThumbsButton and showThumbsOnLoad in the gallery's embedding code accordingly.
Create a sample gallery in JuiceboxBuilder-Pro and replace the gallery's 'index.html' file 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 windowWidth = window.innerWidth ? window.innerWidth : $(window).width();
            var showThumbs = windowWidth >= 640;
            new juicebox({
                containerId: 'juicebox-container',
                showThumbsButton: showThumbs,
                showThumbsOnLoad: showThumbs
            });
        </script>
        <title>Test</title>
    </head>
    <body>
        <div id="juicebox-container"></div>
    </body>
</html>

We have just released a hotfix version of v1.4.0 which includes a fix for the problem you reported (the largeImageURL overriding the linkURL).
Details on how to get the latest version can be found on the Upgrading Juicebox support page.

Thank you for providing the URL to your gallery via email.
It looks like the data for your gallery's XML file is being generated correctly so all the correct files are in place and not corrupt.
However, the problem seems to be that the XML declaration in the dynamically generated XML file (the <?xml version="1.0" encoding="UTF-8"?> line) is not at the very top of the document. There is a blank line before the XML declaration which should not be there and this is very likely to be the cause of the problem.

I cannot be certain but I suspect this may be a bug in the version of PHP which is installed on your web server.
(What version of PHP is installed on your web server and has your web host recently upgraded the version of PHP or changed any PHP settings?)
Please try the following suggestion which should hopefully solve your problem:

Open the module's 'juicebox/includes/JuiceboxGallery.inc' file in a plain text editor and change line 171 from:

return $dom->saveXML();

... to:

return $dom->saveXML($juicebox);

Please note that the line number above refers to the recommended release of the module (dated 2014-Jan-28) which is available from this web page.

Something must have changed for this to happen.
If you did not change anything yourself, then check to see if any automatic updates to your Drupal installation were installed.
Also, check with your web server to see if they have changed anything recently (such as upgrading the version of PHP installed or changing any PHP settings) which may be contributing to your problem.

It would be much easier to troubleshoot your scenario if you were able to provide the URL to the gallery in question so that I could take a look for myself. Without seeing your gallery's embedding code, I have no way of knowing how the path to your gallery's XML file is defined.
It sounds like the PHP file within the Drupal module which dynamically generates the XML data may have somehow become corrupt or missing but, if this were the case, then re-uploading the module's files to your web server (which you have already tried) should solve the problem.

These files and folders are unique to each individual gallery and it is not necessary to copy them into the module's own file structure. (The module deals with these files and folders each time you create a gallery.) Only the 'jbcore' folder should be integrated within the module.

As we did not write the module ourselves (and the problem you are encountering seems to be related to the gallery's embedding code which is generated by the module), you might also like to post in the Drupal forum where the author of the module should be able to help.

However, if you continue to experience difficulties, please post back with the URL to your gallery and I will certainly try to help further.

If/when this happens again, please zip the 'presets' folder and email it to me (I have sent you a message regarding another forum query so you should have my email address) before you trash it so that I can take a look for myself and try to replicate the problem. Thank you.