Hi TnPtech,
The IP Office is your SIP server usually if everything you're doing is local. Also, if you've been only been using h323 phones and now you have SIP phones you'll have to turn on the SIP registration in the IP Office as well. I hope you've done that (SIP trunks enable for SIP trunks and SIP registrar for phones)
There is a LOT to process here, so I'll try and break down my suggestions. I have seen the J179 and J189 phones on the latest firmware not want to connect unless they have the TLSSRVR settings also added. In the past these weren't used but now we have them on all of our client DHCP servers.
We never use the WAN port. Far easier to set your own tagged VLAN on the switches for the phones, we like to use VLAN 200, and you set the switch to have your phone system natively on that VLAN for the just that LAN port and all of the phones on tagged ports on your switches to that VLAN. That way your phones can be on any port and you won't care and they'll be happy in any building on any port. If you have many phones with devices on the same subnet you'll max it out, so better to keep them separate and happy on their own.
You can use the DHCP in the IP Office or your own DHCP server. I'm going to give you an example of the DHCP settings you'll need if you're using your own DHCP server.
MCIPADD=10.0.200.5,MCPORT=1719,VLANTEST=0,HTTPSRVR=10.0.200.5,L2Q=1,L2QVLAN=200,TFTPSRVR=10.0.200.5,TLSSRVR=10.0.200.5
MCIPADD is your phone system, HTTP is for your phone system for upgrades, L2Q=1 is turn on vlan and L2QVLAN is the vlan for the phones to use, TFTP is for upgrades from your phone system and the last one, which I believe might be part of your problem, is for the https link to the IP Office.
You MUST give out the 176 and the 242 options in DHCP for this to work properly.
The Avaya IP Office will do all of this for you if you're using it for DHCP.
As I said, on the newer phones without that TLSSRVR setting they'll just refuse to cooperate until they get that setting and then they'll play nicely again. I hope your issue is that simple!