Juicebox displays images using standard <img> tags (generated dynamically via the 'juicebox.js' JavaScript file) and the image orientation is handled by the browser. Juicebox does not rotate images itself. This applies to both Juicebox-Lite and Juicebox-Pro.

However, JuiceboxBuilder-Lite and JuiceboxBuilder-Pro (the standalone applications to create and edit galleries) both have the ability to rotate images at the time the gallery is created or edited. (See the 'rotate' arrow near the lower-right corner of the first screenshot on the JuiceboxBuilder Tour page.)
When resizing images for a gallery, JuiceboxBuilder strips out all metadata (including the EXIF orientation flag) so browsers will not see an EXIF orientation flag and will just display the images as they are. As long as the images are rotated correctly in JuiceboxBuilder, they should be displayed correctly in the gallery.

Unfortunately, as you are not using JuiceboxBuilder, you'll need to find an alternate way to remove the EXIF data.
I've just tried 'Remove Properties and Personal Information -> Create a copy with all possible properties removed' via Windows 10 File Explorer and it does not seems to remove all EXIF data (the EXIF orientation flag remains).
It would be better to use a dedicated imaging program to re-save your images without EXIF data.
If you do not have Adobe Photoshop or Adobe Lightroom, you could try a free alternative such as GIMP, IrfanView or XnView.
Instructions for removing EXIF data using GIMP can be found on this web page.

I hope this helps.

If you continue to experience difficulties, it might help if I could see one of the source images that is causing you problems so please post back with a link to one of your images so that I can take a look for myself and hopefully help further.