It sounds like the problem you are experiencing is due to the EXIF orientation flags (metadata) embedded within your images (and some devices, most notably phones rather than dedicated cameras, do not seem to set the EXIF orientation flag correctly).

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-Pro) do not read EXIF information and just display the image as it is.
Unfortunately, there seems to be little consistency in how the EXIF orientation flag is handled in different programs.

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 every scenario.
This link (whilst a little out of date now) certainly makes for interesting reading.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 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.

JuiceboxBuilder-Pro has the ability to rotate images on the 'Images' tab (see the 'Rotate' arrow near the lower right of the screen in the first screenshot on this page) so you can rotate images within JuiceboxBuilder-Pro without the need to re-save them without the EXIF information first.

I hope this helps to clarify things a little.