Major Problems with NBT through all versions

I am having a major problem that has really existed since I created my wordpress network, so as far as I know, it has never really worked.

Here is what I have done.
I created a brand-new clean blog, assigned a brand-new never been used before theme. Filled it with content, created menus, assigned widgets to appropriate widget areas, etc.

I then created a "Blog Template" from this blog ID (67). I then went and created a NEW blog chose this template and went to verify the results.

1.) Wordpress Menu Areas are NOT being set, I have to manually go back and set all menus in their appropriate areas

2.) Widgets are jumping to DIFFERENT widget areas, they seem to shift down 2-3 widget areas.

3.) None of the tables I am choosing to copy in Advanced are actually copying... Gravity Forms tables are not copying, Redirection plugin tables are not copying, no plugin tables that are checked are copying.

4.) Additional settings for my theme and my custom configurator (Which are stored in wp_options) are being lost during the clone.

Any ideas what is going wrong here? I am using the latest version of Multi-DB as well, I assume this adds to the complication.