As you have discovered, JuiceboxBuilder-Pro does not use the EXIF orientation flag embedded within images. When images are added to a gallery, the EXIF orientation flag is not read and, when images are resized for galleries, all metadata is removed from the images.
If you need metadata to be retained in gallery images, you could resize your images in an imaging program such as Adobe Photoshop (retaining metadata during the resizing process) before feeding them to JuiceboxBuilder-Pro and deselect the 'Resize Images' checkbox so that JuiceboxBuilder-Pro does not process the images further.
However, this still might not be enough to solve orientation issues. It can be difficult to know exactly how a certain program will display an image with an EXIF orientation flag and there seems to be little consistency across different programs (and web browsers).
For example, try viewing this image directly in different browsers.
http://7stripes.esy.es/sample/image001.jpg
In Edge and IE11, the image is displayed in landscape orientation (the EXIF tag not being read).
However, in Chrome, Firefox and Opera, the image is displayed in portrait orientation (correct according to the EXIF orientation tag which I changed by rotating the image in Windows File Explorer).
When the image is displayed by an HTML <img> tag (just as Juicebox does in a gallery's web page), all browsers (at least the ones I listed above) do not seem to respect the EXIF orientation tag and just display the image as it is.
http://7stripes.esy.es/sample/index.html
You could try including the image-orientation: from-image; CSS rule in your gallery's web page (applied to all 'img' tags) but browser support is currently limited (to Firefox 26 and later) and Juicebox itself would not know that the image had been rotated by the browser which may result in the image being displayed in the gallery with unexpected dimensions (the drop-shadow around the image may be in an incorrect position).
With all this in mind, perhaps the best way to ensure that your images are displayed as expected in your gallery would be to re-save your images in an imaging program (such as Adobe Photoshop), stripping out the metadata during the resizing process and then rotate your images so that they are visually oriented correctly (inverting their actual aspect ratios rather than introducing new EXIF orientation flags) before feeding them to JuiceboxBuilder-Pro.
EXIF orientation can be a minefield at times and, as can be seen above, it is not always easy to predict how an image will be displayed in any given program.
This article, whilst a little out-of-date, makes for interesting reading.
Knowing how JuiceboxBuilder-Pro works should at least allow you to adjust your workflow to obtain a gallery with correctly orientated images.
If you do not have Adobe Photoshop, then there are other imaging programs you could use to batch process (re-save with or without metadata, rotate, etc.) your images, such as Irfanview. (This is just a personal suggestion rather than an official recommendation.)
I hope this goes some way towards explaining things.
Can you please not strip out whatever information is in the photo files that indicates their correct orientation??
I do not know how likely it is that JuiceboxBuilder-Pro's behavior will be changed in the future but, if you like, please feel free to make suggestions for future versions in the Feature Requests forum thread.
This keeps all the ideas together and ensures that they are not overlooked by the developers.
Thank you.