Some imaging programs such as Adobe Photoshop have the ability to read the EXIF orientation flag and display the image in the orientation specified by the flag but other programs (such as JuiceboxBuilder-Lite) do not read EXIF information and just display the image as it is.
Unfortunately, there is little consistency, even between different web browsers.
If you are having problems with the orientation of a specific image and view it directly in Mozilla Firefox, (if you drag and drop the image into an open tab or window), you will likely see your image displayed in a different orientation than if you were to open the same image in Google Chrome.
Unfortunately, no matter what decision is taken regarding EXIF orientation (whether or not to use it at all and, if using it, how to interpret it) there seems to be no single solution which will work for everyone.
This link (whilst a little out of date now) certainly makes for interesting reading.
The only way to ensure that your images will be displayed as you expect in all browsers and programs would be to strip the EXIF information from the images (by re-saving the images in an imaging program and choosing not to keep the EXIF information) and then rotate your images until they visibly look correct.
However, JuiceboxBuilder-Lite does have the ability to rotate images on the 'Images' tab (see the 'Rotate' arrow near the lower-right corner of the screen in the first screenshot on this page) so you can rotate images within JuiceboxBuilder-Lite without the need to re-save them without the EXIF information first.
I hope this helps.