How does adding custom meta to signup form work?

I had this same problem and I found that the blogtemplates plugin was deleting my options after I updated them. You may have a similar situation.

I fixed my case by making my wpmu_new_blog hook execute after blog templates.

    // blogtemplates executes at 9999, go last at 10000
    add_action('wpmu_new_blog', 'process_extra_field_on_blog_signup', 10000, 6);