Hello. Thank you for purchasing Showkase!
As you have discovered, all Juicebox galleries within a Showkase site share a single 'jbcore' folder which means that all Juicebox galleries share the same 'pswd.php' file (i.e. all galleries have the same password or passwords). (The array in the 'pswd.php' file simply allows a variety of passwords to be used for a single gallery.)
Unfortunately, there's really no quick and easy solution to allow each gallery to have it's own unique password.
In order for each gallery to have its own 'jbcore' folder, the Showkase source would need to be modified significantly and, in order for Juicebox to support multiple passwordsand map them to different galleries, the Juicebox source code would need to be modified (and this is not something that a user can do, please see this FAQ for details).
However, there is something that you might be able to do.
As each Showkase page has its own folder (in the root Showkase directory), you could password-protect each gallery folder at server level, using .htaccess and .htpasswd files or from within your web hosting account's online control panel.
It maybe not quite as convenient as if Juicebox/Showkase allowed individual gallery passwords but as long as your web hosting account's online control panel allows you to password-protect individual directories, it should actually be quite quick and easy to set up. (Log into your control panel and what you're looking for might be labelled something like 'File -> Directory Privacy').
I hope this is a suitable workaround for you as the alternative (modifying Showkase and/or Juicebox) would really be much more difficult that it might seem at first glance.