Hi, I'm not sure you're having the same problem as I was but it's worth a try!
I was setting two DNS servers (two piholes) using dnsmasq.d config file and the way to do it now is to add the lines here: Settings > All Settings > Misc > misc.dnsmasq_lines
What I had to write was dhcp-option=option:dns-server,192.168.0.99,192.168.0.77 (2 adresses because 2 piholes)
You should try with your ServerIP so it should look like dhcp-option=option:dns-server,192.168.0.99 (replace 192.168.0.99 with your ServerIP)