Hi James.
Both IAP's are setup to be managed in VLAN 2,
IAP1: 172.18.24.220
IAP2: 172.18.24.221
Virtual Controller: 172.18.24.222
Then we have two SSID's one using VLAN 6, the other VLAN 100.
I have set the wired profile to a trunk port, with the native VLAN set as 2, and allowing 'all' VLANs.
I decided to reset one IAP and now it will not join to the Virtual Controller already on the network, so I now have two standalone IAP's, not ideal but it is working. I have a feeling we have a layer 2 issue, because both IAP's are on the same country code and auto join is definetely enabled at the GUI.