The 'Export' and 'Upload' buttons are part of Lightroom (rather than the Juicebox plugin) and their functionality is controlled purely by Lightroom itself. Try using a different web engine (such as the default 'Lightroom HTML Gallery') and you should see the same behavior.
If you want to save a gallery to an existing folder (for example to overwrite an existing gallery), then click the 'Export' button, navigate into the folder's parent directory, highlight (single left-click) the folder you want to save your gallery to and click the 'Choose Selected' button (rather than the 'Open/Save' button). You should then be notified that files may be overwritten.
I hope this helps.