Alright, so I got the server to start finding all the subnets. I had to change my active discovery subnets from theĀ /16 subnet, to two /24 subnets. I guess a /16 is just too large an address space for the server to search through in a timely fashion (especially since most of the subnet space it was looking at, was non-existent).
The only issue that is left is that not a single node that it discovers, does it discover it with the proper subnet. It is finding everything as a /32 instead of /24...so right now what I have to do is go in and stop the server, manually change the subnets in the database, then start the server back up. At this point all the hidden nodes start showing up and going in their correct groups.