New versions of both Lite and Pro include some important bug fixes and also add use of capabilities for creating admin menu for the plugin. Only administrator role is given this capability by default. There are new translations in Lite and more features in Pro.
Pro version includes several bugs fixed, including bug that was fixed in both Pro and Lite preventing settings custom taxonomy rewrite slug that contain slash character.
Major change are added settings to globally enable or disable special features added by Pro edition for custom post types and custom taxonomies. In some rare cases, Home Page special feature can conflict with other plugins. This special feature adds posts from custom taxonomies to home page loop. In some cases this will not work, and now you can disable whole feature from Settings panel, Special Features tab. Other special features should be safe to use in any case, but you can disable them also. If you have problem with disappearing content on home or posts pages, disable this feature.
If you have any more problems, please report them in the forum or in comments.
GD Custom Posts And Taxonomies Tools: