Thank you for reporting these two bugs.
I have notified the developers and hopefully they will be fixed in the next version of Juicebox.
In the meantime, one possible workaround would be to set showInfoButton="TRUE". The overlay would still be able to be toggled on and off by the user but the hit area would be much smaller (the Info Button on the button bar instead of the entire mobile device screen) and this should also solve the problem with the missing image navigation buttons when the overlay is toggled back on (which could also be solved by setting imageNavPosition="STAGE").

If you have found a workflow that works for you (and results in a gallery with your images oriented correctly) then I would recommend that you continue using it.
As you have discovered, the rotation functionality within JuiceboxBuilder is available for individual images only (and not for a selection of images).
Also, as you suspect, different camera and mobile device manufacturers have been known to signify similar orientations with different (incorrect) EXIF orientation values. This can lead to further confusion and problems when dealing with such data.
Please post any suggestions for future versions of Juicebox, in the Feature Requests forum thread. This keeps them all together and ensures that they are not overlooked. Thank you.

The # anchor links that Juicebox uses are dynamic and do not correspond to actual # sections within the web page.
For example this URL http://www.example.com/gallery/#4 would link directly to the 4th image in the gallery but there is no actual '#4' entry on the web page. (Juicebox's 'juicebox.js' JavaScript file reads the URL, figures out what the #4 means and displays the image dynamically.)
The way this works is the same whether sharing is enabled or enableDirectLinks="TRUE".
For this reason, I think it is unlikely that Google would be able to index and list individual images in a gallery, each with its own unique URL.
I think the best that you could do would be to ensure that you include SEO content in your web page and have your images indexed by Google but all pointing to the gallery page.

It looks like your Flickr User Name may be 'Goran Beg' rather than 'goranbeg'.
Try this instead.

The problem with your 'thendara' galleries seems to be the text-indent: 5px; entry on line 209 of your http://www.thendara.co.uk/style.css file.
If you remove this line from the .container_12 .grid_3 section of the file, your gallery's navigation arrows should be in their correct positions.

The error you reported above is more of a warning than a problem and is not going to be the cause of a flickering gallery.
It looks like you may have deleted your original post in this thread (it certainly seems to have disappeared).

Does the flickering occur when you view the gallery on its own web page (when you view the gallery's own 'index.html' page inside the gallery folder) or just when the gallery is embedded in your main page?
Also, does your button bar disappear when expanding the gallery from its own web page or just when expanding the gallery from your main page.

If you have any add-ons installed in IE11, try temporarily disabling them to see if this makes a difference.

If you continue to experience difficulties, please explain exactly what the flickering looks like (do images quickly appear and disappear, is it just the main image or the whole gallery) and at what point in the gallery the flickering occurs (when the gallery is initially loaded or at the start or end of an image transition or when clicking a button on the Button Barl).

OK. I'm glad everything seems to be working as expected again. Thank you for letting me know.

What you are describing here is the Splash Page (which is displayed by default in Small Screen Mode or if showSplashPage="ALWAYS"). You can find more information about the Splash Page in the Screen Modes section of the Gallery Tour.

@joaqimb

I have viewed your Boogieboy and Namur galleries in Internet Explorer 11 and I do not see a flickering image and the Button Bar appears at the upper-right corner of the expanded gallery. Everything appears to be working as expected.
If these are not the galleries you are referring to, then please post the URL to the gallery in question and let me know what version of Internet Explorer you use.

The following are general tips which may help with the symptoms you describe but if the galleries I named above are the ones you are referring to, then the problem may be local to your computer or the version of Internet Explorer that you use.

First of all, please ensure that you are using the latest version of Juicebox-Pro (v1.4.2).
Instructions for upgrading can be found here.

Please see this FAQ, which may help: My gallery looks strange in Internet Explorer 9. Why?

Also, please make sure that your Internet Explorer browser is not displaying your web page in Compatibility View.

Next, check your web page for any HTML errors. You can check the code on your web page with the W3C Markup Validation Service and then fix any errors reported. Once the code on your web page validates correctly, your web page should be rendered with greater predictability and consistency across different browsers.

Try one (or more) of the following:

• Try setting a fully opaque expandedBackgroundColor (such as expandedBackgroundColor="rgba(255,255,255,1)") in JuiceboxBuilder-Pro's 'Customize -> Color' section (set the 'Opacity' value to '1').

• Try setting expandInNewPage="TRUE" in JuiceboxBuilder-Pro's 'Customize -> General' section.

• Try changing the useFullscreenExpand configuration option (from TRUE to FALSE or vice versa) in JuiceboxBuilder-Pro's 'Customize -> Lite' section.

If you want to reverse the order of images in a Media Library gallery, edit your gallery (on the 'Dashboard -> WP-Juicebox -> Manage Galleries' page) and select either 'Ascending' or 'Descending' (whichever is appropriate) for the 'Image Order'.

The images are ordered by the WordPress 'menu_order' so the images should be displayed in the gallery as they are listed in the 'Insert Media -> Media Library -> Uploaded to this post' display (or in reverse order if selected in the gallery settings).

If you want to reorder images in a gallery (more than just reversing the order), then edit the page or post containing the gallery, click the 'Add Media' button, select 'Insert Media -> Media Library -> Uploaded to this post' and drag and drop the thumbnails into the order you would like them to be displayed in your gallery.

I have taken a look at your web site and have found your gallery's web page.
The problem is that you have entered your embedding code into your Drupal editor as plain text and not as HTML code (and the embedding code is appearing as text on your web page rather than being rendered as actual HTML code by the browser).
You will need to change your editor's 'Text format' (at the bottom of the editor) from 'Plain text' to 'Full HTML' before entering the embedding code.

This is not the problem (see above) but you can change the name of the page to anything you like (to avoid filename conflicts).
If you are embedding your gallery in an existing web page, then you do not need to use (or upload) the gallery's own 'index.html' file at all. It is used only if you want to display the gallery on a page of its own.
Also, the 'index.html' file will be stored within the gallery folder and if you use a baseUrl, you will upload the entire gallery folder (not just the contents) so there is no chance that the gallery's 'index.html' file will conflict with one of your own 'index.html' files.

On your web server, the root directory is 'public_html'.
If you upload a file named 'test.html' to your 'public_html' directory via FTP, then it will be accessible on the web at '/test.html' in one of your web pages.

This fails within the forum software because you use a space in your 'Juicebox Namur' folder name (and the forum software sees a space as the end of the path). As long as the paths are correct within your web page, everything should be OK.
However, I would recommend that you use only web-safe characters for files and folders on your web server.
Please see section 2.3 of this document for details.

It looks like the root of your problem lies with your external 'parallax.js' JavaScript file.
When it is loaded in your web page, it removes (rather than just hides) the following elements from your web page's Document Object Model (DOM).

story-home
story-live
story-travel
story-explore
story-about
story-contact

Your 'Live' gallery's container ('livecontainer') is within the 'story-live' <section> and your Travel gallery's container ('travelcontainer') is within the 'story-travel' <section>.
When Juicebox tries to loading the galleries into the respective gallery containers, the containers no longer exist on the web page because they have been removed by the code within 'parallax.js'.

The comment on your main web page regarding the 'parallax.js' file suggests that it may cause problems :

I do not know exactly how your web page has been designed to function (over 12 external CSS and JavaScript files are loaded on your page so it is difficult to see exactly what is going on) but if your web page somehow reinstates the elements which were initially removed by 'parallax.js' (perhaps when links are clicked), then the solution to your problem would be to delay loading your galleries until such a time that the required gallery containers are present and part of the DOM.
You could put your gallery's embedding code into a JavaScript function and run the function when a link is clicked using a jQuery .click() handler (as your web page already loads and uses jQuery).

Otherwise, an alternative would be to fiond a solution which does not use 'parallax.js'.

This might be because 'parallax.js' removes DOM elements which are not initially displayed on screen (initially hidden by and accessed via a menu system) when the web page is loaded.