Hi AJ,
> Also, just curious, but it seems that I don't need "MB Custom Post Types & Custom Taxonomies" or "MB Relationships" as separate plugins if I have Meta Box and Meta Box AIO activated. Is that correct?
Yes, that's right. AIO already includes those plugins.
Regarding your issue, I think the problem was in the 2.6.x version of MB Custom Post Types & Custom Taxonomies plugin. We released version 2.6.0 which had a new feature to allow you to edit post types registered in WP core (like post and page) and post types registered by other plugins. The way it works is replicating those post types in the plugin's post type list, so you can edit them as usual.
I *guess* in your case, when you upgraded the plugin, it replicated some post types registered by other plugin. Those post types had some rewrite options that were available in MB Custom Post Types & Custom Taxonomies and caused the bug.
We reverted this feature in 2.6.2, but the replicated post types are still in the DB.
One way to resolve this is go to Post Types and remove all post types that were not created by you manually. The other way is what you did by updating the settings for them.
I hope this clarifies things and what happended behind the scene.
.
