I was able to fix this. I moved the sunrise.pgp file to above the last require_once() line in addition to copying the sunrise.php file from wp-content/plugins/wordpress-mu-domain-mapping/sunrise.php to wp-content/sunrise.php.
Then I made sure that the sites were set up properly within domain mapping (which the 2 were not).
I think some of the files were re-written with the plugin update and had to re-set up the two sites.
Hope this can help someone else!