GD Custom Posts And Taxonomies Tools Pro 3.6.6 is released to fix the issue caused by some changes in WordPress 3.4 with Rewrite class. Because of that, custom permalinks for custom post types stopped working when upgraded to WordPress 3.4. Few more warnings are also fixed.
To make sure that new version is working OK, you need to regenerate rewrite rules. You can do it from the plugin Tools panel (WordPress rewrite rules Reset), or from WordPress Permalinks panel. Also, some warnings with taxonomies classes were fixed (nothing critical, simply, variables that were not initialized).
If you notice any more problems with the plugin, please report them in comments or forum.