Ah ha! Found it I think. I was finally able to replicate the problem locally and play with it more.
It turns out that the following line was below the absolute path stuff (below the "That's all, stop editing!" line).
define('WP_ALLOW_MULTISITE', true);
I also had to add in the following line below that:
define( 'MULTISITE', true );
I think because my site was wordpress mu when we started it was not included. I thought just adding in the first part would work. But it requires both to work correctly. I am pushing this fix out to our dev environment now and will confirm if it is working as expected after this.