As long as you are following the Install a Pro Viewer instructions, all your Juicebox galleries should be upgraded successfully.
After republishing your site, try clearing your browser's cache to ensure that your browser uses the most recent versions of your gallery files.
If you like, please post the URL to your gallery's web page so that I can take a look. I'll report back to let you know what I see (Juicebox-Lite or Juicebox-Pro) and if I find anything odd with your Showkase installation.
Incidentally, if you have Showkase-Pro (rather than Showkase-Standard), then you might like to try upgrading Showkase-Pro itself. The current version of Showkase-Pro (v1.6.1) comes bundled with the latest version of Juicebox-Pro (v1.5.1).