I’m not sure (just an hypothesis), but it looks like the new version (1.1.6) only looks in the wp_sitemeta table for all options in a multisite config. Maybe you can copy your AD_Integration_% rows from wp_options or wp_?_otions table in wpsitemeta table.
Looks to me like the new v1.1.6 will BREAK many installation where we need to have AD groups specific for each site.