Why does the linking get lost when copying over theme option data?

I am using a theme NS Cloner - Site Copier to clone an existing primary site so I can use the new blog template to replicate. When I do this my theme option data does not appear. I can go directly into the table and paste it but it is still not available. I can save it through the theme options page and it is available. I am hoping that I do not have to do this for every site. Any help on understanding this?