Hi all, apologies, in my haste I've led to confusion, didn't have a lot of time to post so threw up that diagram, to answer some of your questions:
MAC address binding it for management hosting of different things on different clients, it's not essential and I switched it off while testing for a while.
VLAN management can be ignored, I was trying to give a scope of the network as I have no idea why this is happening but I don't think it's to do with VLAN. This part of the network is all on the same VLAN anyway and the router is set to allow all non tagged traffic on to this subnet (even if it doesn't support VLAN tagging).
Main Room:
Router = Draytek Vigor 2860
IP address is 192.168.1.254, the LAN range denoted by CIDR is 192.168.1.254/24 (so subnet mask is 255.255.255.0).
DHCP is on (but I have IP to MAC binding enabled so clients keep their IP's. I have some on static IP outside of the DHCP pool, I.E. the Pi-Hole but this is probably not important.
DNS for DHCP clients is set to the PI-Hole.
Due to VLAN and VPN I have to use this DHCP server.
Second Room:
Wireless AP (It doesn't perform NAT, it's not a router).
The second device is a TP-Link WiFi extender, it has two modes, wireless extender (forwards WiFi packets) or WiFi access point (ethernet bridge). It is set up as a WiFi access point. Connected via ethernet to port 1 on the router (VLAN 1/Same subnet) through the powerline adaptors and has a static IP set up: 192.168.1.253, subnet mask 255.255.255.0, DNS set to Pi-Hole (for it's own traffic).
DHCP server is off on this device, so clients obtain DHCP information from the Router 1. This does work, but like I said, when I switch clients from the Wireless AP, to Router 1 SSID (they have different SID's, on different channels), the clients have no networking, I have to reboot them or reboot the whole network.
I guess I'm a little confused with your diagram. Router 2, is shown as "DHCP: Disabled", but yet, "DNS: PI-Hole (IP)"? If DHCP is truely disabled, it's not going to be handing out DNS server IPs to clients with PI-Hole (IP). Do you mean that the router's own DNS is set to the PI-Hole? If so, consider setting that to Router 1 as the DNS server for Router 2. (Router's OWN DNS server, not the DNS server handed out via DHCP to clients, right?)
I'm not sure I see the point in this VirtualLarry, the problem is not while connected to the Wireless AP but when going from the AP SSID to the Router SSID, this would also negate the DNS filtering from the PI-Hole and lead to a DNS leak, and I don't think this is a DNS issue as IP's can't be resolved by lookups either when the clients have no networking.
To outline the problem:
1. I connect my laptop or mobile to the router WiFi, everything is working.
2. I walk in to the other room, my device connects to the AP wifi, everything is working, my IP is the same as on the previous WiFi due to IP to MAC binding etc, DNS is routing properly through the PI-Hole, etc. Everything working how it's supposed to.
3. I walk back in to the main room with the Router and connect to it's WiFi again. It connects, I have the same IP as before, but no traffic, no response to pings internally using hostame or IP, no internet. If I'm on a PC and perform an ipconfig/release/renew it does nothing, it waits and waits. It's like it's connected but not connected. If I remember correctly while testing on Sunday night, on a few occasions I could ping the Router while the clients in this state but nothing else, most of the time I couldn't ping anything. Oddly when I reboot the client, the issue goes away, until I connect to the Wireless AP again, rinse and repeat. I think this might be some layer 2 issue or something but I'm out of my depth.