I recently upgraded WordPress to version 3.2 and then I also updated to the latest version of GD custom posts and taxonomies tools (1.4.0), and now when I add a new post type, the Features and Taxonomies fields don't change when I make changes to them. The taxonomies field shows that I removed all the taxonomies from my new post type, but then I save the page and they all come back to the new custom post type. The same issue happens with the Features field.
I have an older custom post type (which was created in an older version of the plugin), and that post type still retains all the changes that I made to it. The issue only came up when I upgraded WordPress and this plugin. I can still save the new custom post type and it shows up in the admin area, but it won't save any of the changes to Features and Taxonomies.
Hopefully that is thorough enough. Thank you!