It sounds like you might be using the Juicebox plugin for Lightroom (Lightroom has a button labelled 'Export...' unlike JuiceboxBuilder-Pro). If not, then please let me know.

After clicking 'Export', either:

(1) Navigate to the parent folder where you'd like to save your gallery folder to, enter a name for your gallery folder and click 'Save'. The gallery will be saved to this new folder.

... or:

(2) Select an existing folder that you'd like to save your gallery to and click 'Choose Selected'. You will then see an 'Overwrite Confirmation' dialog box and, after agreeing (by clicking 'Proceed'), any existing files within the folder with similar filenames will be overwritten. (There should be no duplicate files with different filenames within the folder.) The gallery will be saved to the selected folder.

(Incidentally, this export procedure is core Lightroom functionality rather than any code specific to the Juicebox plugin.)

I hope this helps to clarify things.
However, if this does not help with your problem, then please let me know and I'll try to help further.
Please let me know what program you are using to create your Juicebox gallery and the names of the files that appear in your gallery folder. Are all gallery files (and/or folders) duplicated (including 'index.html', 'config.xml' and 'jbcore') or just image files? How are the duplicate files named (do they have suffixes such as (1), (2) or _1, _2? Knowing how the duplicate files are named might help to figure out what program is renaming them.
Thank you.