I noticed and had pointed out several issue with the latest release of Lightbox Plus. I am planning on releasing another version today that will hopefully recify the issues.
The upgrade was not removing the old unneccesary files from the plugin – the plugin needs re-initialization at least once upon upgrading. This will now remove old Lightbox Plus files assuming you have the correct permissions on you server to do so. Otherwise you must manually remove the following files and directories:
This will give you a clean install. You will still want to re-initialize or set and save the settings for Lightbox Plus before proceeding.