I just upgraded to vers 2.0.6 - and now all my custom sidebar positions are thrown. Not only that, but when I try to position them again, on the post-types and categories I need, I don't get the option of any categories or post types.
I hope the values I set previously are in the database still and haven't been lost. I also hope you're working on this and will soon provide another upgrade which will once again give me access to select all my CPTs and taxonomies for selecting where to place my custom sidebars.
I am hours away from launching this site for an important client, so please reassure me.