with the exception of the page/post settings that aren't saving.
You need to deactivate Breadcrumb NavXT and then activate it to fix this issue. There is a migration script for this, but it doesn't run through the plugin updater as the plugin updater is not (as far as I can tell) deactivating the plugin. The post_post_OPTION is to eliminate collisions with custom post types (all post options are in the form post_POSTTYPENAME_OPTION for custom and default types).
The "network site" type is new to WordPress 3.0, and is not supported yet in 3.6.0, support for that and global sites is slated for Breadcrumb NavXT 3.7.0 (the next major release).