I've deployed three more new multisite environments within the last 6-7 days and all three have the:
define( 'WP_ALLOW_MULTISITE', true );
...twice.
This has got to be an issue with the EE implementation of multisite as I do NOT get this with a standard WordPress deployment, not using EE. @ssalil and @rahul286 please take a look at this, as it is causing problems with SSL deployments.