As long as the 'wp-juicebox' folder is in your WordPress 'plugins' directory (and the 'wp-juicebox.php' file is inside the 'wp-juicebox' folder), then the plugin should be listed on your Dashboard -> Plugins page.
Please double-check that the 'wp-juicebox' folder is in the correct location on your web server.
The theme you use should have no bearing on whether or not a plugin shows up in the list but, being that you are experiencing difficulties, you could try temporarily reverting to the default WordPress theme to see if this makes a difference.
I would be happy to offer more help but in order to investigate further, I would need to see the problem for myself which would require access to your WordPress installation and your web server.
If you are agreeable to this, then please email me the URL and login details to your WordPress installation and the FTP login details to your web server and I will take a look and try to figure out why the plugin is not showing up.
In the meantime, if you like, you can manually embed Juicebox galleries into your WordPress pages or posts using the baseUrl method of embedding as documented here.
Essentially, you would create a Juicebox-Pro gallery using JuiceboxBuilder-Pro, upload your entire Juicebox gallery folder (not just the contents) to your web server and then 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) are correct.