Here are a few tips which might help.

(1) When embedding multiple galleries which may be displayed on the same page (perhaps on  the home page of a WordPress site), you'll need to ensure that each gallery is embedded into a container with a unique containerId and corresponding <div> 'id'.

(2) Also, when embedding multiple galleries into a single HTML web page, the 'juicebox.js' file should be loaded only once per web page rather than once per gallery so, in a WordPress environment, it would be wise to load the 'juicebox.js' file once via your theme (rather than in each gallery's embedding code).

(3) Depending on the permalink structure of your WordPress site, it can be difficult to know exactly where to upload your gallery files. In order to combat this, I'd recommend using the baseUrl method of embedding documented here.
The baseUrl method of embedding is basically the same as the regular method but with a baseUrl entry in the embedding code pointing towards the gallery folder.
Essentially, once you have created a Juicebox gallery on your computer with JuiceboxBuilder-Pro, you would upload the complete gallery folder to your web server and paste the baseUrl embedding code into the body of your WordPress page or post (ensuring that the method of entry is 'Text' rather than 'Visual'). It does not matter where on your web server you upload your gallery folder to as long as the two paths in the embedding code (the path to the 'juicebox.js' file and the baseUrl itself, pointing towards the gallery folder) are correct.
For example, you could upload a gallery folder named "my_gallery" to your root directory and then just add baseUrl="/my_gallery/" to the gallery's embedding code. (The leading slash in the path denotes your root directory so this baseUrl will work in any web page throughout your site without modification.)

Rather than embed your galleries into your WordPress pages and posts manually, You might like to try using the dedicated Juicebox plugin for WordPress (WP-Juicebox) which automatically takes care of all three of the points mentioned above.
Instructions for downloading, installing and using WP-Juicebox can be found on the plugin's support page here.

I hope these notes help.
However, if you continue to experience difficulties, please post the URL to one of the gallery pages that you are having problems with and I'll take a look and hopefully help further. Thank you.