I am having the same issue after the most recent Pi-hole update (rate limit message for router's IP address). I have a ZyXel router provided by my ISP.
I'm not sure yet if this is the problem but DHCP on the ZyXel doesn't seem to hand out DNS entries to clients correctly. The clients are not getting the DNS entries the way I have them configured. It wants to force one of them to be the router IP, even though I have all of them set to either the Pi-hole address or "none".
Edit: Switching DHCP to the Pi-hole stopped the rate limiting message. My guess is that the way the ZyXel forces its own IP to be one of the DNS addresses handed out by DHCP causes a loop.