The AP's have previously been working, and we have gone through a fairly major network upgrade changing our core switches to Juniper from Cisco. The issue had existed before this changeover started, and kind of started spreading during the switch.
From a network perspective, there is no access-list applied to any of the interface vlan's that would block this traffic. I can ping both the AP, and the controller with a source IP of the interface vlan. They are authenticating in ACS.. The list goes on, if you have more specific questions I can definitely answer you.
As mentioned in my other response, they are discovering the controller with DHCP.