I am glad you have been able to resolve your problem.
Thank you for posting back to let me know.

When using the Lightroom plugin, all options are intended to be set via the interface.
Default options are stored in the 'galleryInfo.lrweb' file which is compiled and cannot be modified but if you change any settings in the interface, they should be remembered the next time you open Lightroom.
If you like, you can override the interface and set a value to be used in all galleries by modifying the 'config.xml' file in the 'juicebox.lrwebengine' folder.
For example, to use thumbnail dots in all galleries, change:

useThumbDots="<%= model.nonCSS.jb_useThumbDots %>"

... to:

useThumbDots="TRUE"

In this example, the 'Use Thumbnail Dots' checkbox will be ignored in the interface and useThumbnailDots="TRUE" will be used in all galleries created by the plugin.

Please see Step #4 in the 'Upgrading to Juicebox-Pro' section on the Lightroom Plugin page.

The background color can be set in a gallery's XML file but because the plugin sets the background color in the embedding code (as in our example code here) it overrides the value in the XML file.
The order of option precedence can be found in the Setting Config Options section.
If you want to set a background color for all galleries, open the 'juicebox.lrwebengine/index.html' file in a plain text editor and change:

backgroundColor: '<%= rgba(model.nonCSS.jb_backgroundColor_, model.nonCSS.jb_backgroundOpacity) %>',

... to:

backgroundColor: '#222222',

... changing the hex color code as appropriate.

It looks like there might have been a problem when uploading your gallery files to your web server.
The images appear to be corrupt. Try viewing the first image in your gallery directly in a browser (bypassing Juicebox entirely):
http://theoff.info/Himalaya/Himachal-Pr … ing-93.jpg
I suspect there are also corrupt Juicebox files on your web server which are contributing to the other visual problems in your gallery.
Try deleting the gallery folder from your web server and re-upload it.

Please note that you should navigate towards the gallery folder (not a file within the folder).
What exactly happens when you try to open your existing gallery?
Does the 'Open Gallery...' button open the 'Select Gallery Folder...' window?
Does JuiceboxBuilder-Pro freeze when trying to open the gallery?
Are any error messages displayed on screen?

JuiceboxBuilder-Pro should save a gallery to the location specified in the 'Gallery Folder' field on the 'Publish...' tab.
You can select the location using the 'Browse...' button.

In all my posts above, I have recommended using a separate PHP file to generate the XML data (so that the code can be accessed and reused from different pages) using the following process:

Your 'original' PHP file would create your main web page including your gallery's embedding code. Within the embedding code you would point towards a different PHP file (using the configUrl configuration option) which would generate the XML data. Once processed by the server, the data output by this PHP file would look just like an XML file to a browser.
The PHP file which would generate the XML data would look something like the file in this forum post.

However, as you suggested, an alternative would be to use a session variable using the following process:

Have the XML data generated in your 'original' PHP file and save the data as a long string in a session variable.
Point towards a different PHP file (using the configUrl configuration option).
In this PHP file, you would simply output the contents of the session variable. The entire PHP file would look something like this:

<?php
header('Content-type: application/xml');
session_start();
echo $_SESSION['xmldata'];
?>

Both methods will work fine but you do need to have your XML data in a separate file (whether it is generated by the file itself or simply passed to the file in a session variable).
It would not be possible to generate the XML code in your 'original' PHP file (which generates the page containing the gallery's embedding code) and pass it directly to the gallery.

Try reducing the line-height for the .jb-caption p entry on line 236 of the Juicebox-Lite v1.3.2 'jbcore/classic/theme.css' file (from its default value of 23px to something lower such as 15px).

Please see this FAQ:
When I view my gallery locally in Google Chrome, I see the message "Juicebox does not display locally in Google Chrome". Why?

You will need to create a completely separate PHP file to generate the XML data for your gallery. This will have nothing to do with your other PHP file which creates your main HTML page and which will include your gallery's embedding code.

The PHP file which generates the XML data will be processed by the server and will output only the XML data required for the gallery. It is this file that you will need to point to within your gallery's embedding code with a configUrl (otherwise, Juicebox will not know where to find the PHP file).

It should be possible to dynamically create an XML file for a Juicebox gallery using most server-side scripting languages as long as you can output the required XML data (though I have not personally tried using a Web API URL as a configUrl).
Perhaps someone else reading this thread has already tried this and can comment.
If you want to try this for yourself, perhaps this web article will help: Getting the Result of ASP.NET Web API in XML Format

When creating a gallery with JuiceboxBuilder-Pro using default settings, the application will resize your images to 1024x768 (with a quality of 80%), resulting in images with a file size of approximately 120KB each.
These default values are usually a good compromise between resolution, quality and file size for web gallery use.
The ideal size for your images will depend on a number of factors including the dimensions of your gallery and the audience you are targeting with your gallery (whether they are likely to be viewing your gallery on mobile devices or on large monitors).
Therefore, 1024x768 may not be ideal for all scenarios but it should be a good starting point for most users.
If you do not want your images to be scaled within your gallery, you can set imageScaleMode="NONE" (in JuiceboxBuilder's 'Customize -> Main Image' section). If using this setting, large images will be cropped to fit the image area.

You can certainly use a PHP file (instead of a static XML file) to dynamically generate a Juicebox gallery's XML file on-the-fly at the time the gallery is displayed/viewed.
An example of how this can be achieved can be found in the answer to Query #3 in this forum post.
Essentially, you would use a PHP file instead of a traditional static XML file and point your Juicebox gallery towards it using the configUrl configuration option.
Your PHP file would need to generate the XML code using the same structure as a standard 'config.xml' file (see the 'juicebox_lite_1.3.2/web/config.xml' file from the Juicebox-Lite download zip package for an example) but you could pull in images and captions from your chosen source by modifying the code as required.

These are questions that should really be directed towards Flickr as only Flickr will know the answers for sure.

I suspect it may take some time for any changes you make to propagate throughout Flickr's servers. I do not know how long it may take but new tags can take up to "a few days" before they appear in API searches according to this Flickr FAQ:

I would certainly expect the time to be taken into account, being that Flick have a time field that you can change.
If you have several images that have exactly the same posted date and time, then my best guess would be that they would be displayed in the order in which the uploads to Flickr completed (although I may be wrong about this).
You might want to post these queries in the Flickr help forum for definitive answers.

The best way to deal with multiple galleries is to keep each gallery in its own separate folder (so that there are no file name conflicts), upload the complete gallery folders (not just the contents) to your web server and embed each gallery using the baseUrl method documented here.