First of all, please see this Juicebox support section on Screen Modes.
Setting showLargeThumbs="FALSE" will initially hide the thumbnails in Large Screen Mode.
If you wish to prevent the viewer of your gallery from ever being able to show the thumbnails, you should also set showThumbsButton="FALSE".
Setting showSmallThumbs="FALSE" will disable both the thumbnail page and the thumbnail button in Small Screen Mode.
All galleries created by WP-Juicebox share the same 'jbcore' folder.
This allows the user to upgrade all galleries in a single action, when a new version of Juicebox is released, by replacing the 'jbcore' folder in the 'wp-plugins/wp-juicebox/' folder.
When WP-Juicebox is enabled, the 'wp-plugins/wp-juicebox/jbcore/juicebox.js' file is automatically loaded on the page.
Therefore, if embedding galleries manually into WordPress (instead of using WP-Juicebox), then you should deactivate WP-Juicebox.
When embedding your gallery manually, your WordPress theme is inserting <p>, </p> and <br /> tags throughout your embedding code.
If you are not already doing so, try inserting your embedding code into your post with the method of entry set to 'HTML' rather than 'Visual'.