Expected Behaviour:
Host names will be blank and only show the IP
Actual Behaviour:
All hosts and showing as pi.hole in the network table and query logs
Your debug log suggests that you are running two DNS servers in your network, one at 192.168.12.3 and one at 192.168.12.4, with the former being the machine hosting the Pi-hole creating the debug log.
What's the output of the following commands:
nslookup mat 192.168.12.2
nslookup mat 192.168.12.3
nslookup mat 192.168.12.4
Hello, thanks for taking a look.
I have two pi holes, 192.168.12.3 and 192.168.12.4. the hostname MAT is a windows server which lives on 192.168.12.12.
Those nslookup results indicate that the machine they were run from is not able to access any of 192.168.12.2 through 192.168.12.4 for DNS.
This would usually suggest a firewall issue.
Make sure that your Pi-hole host machine does not block Pi-hole's required ports.
DNS is working fine, I can resolve hostnames etc. The problem I have is when my pi Hole 1 (192.168.12.3) tries to resolve hostnames of all my local devices. if it cant resolve a hostname it gives them the hsotname pi.hole. This doesnt happen on my Pi-hole 2 (192.168.12.4) on this Pi-hole if it cant resolve a hostname it lives the filed blank
All of your DNS requests failed with time-outs, i.e. there is no DNS resolution at all via 192.168.12.2, 192.168.12.3 or 192.168.12.4, at least from the Windows client that issued those nslookups.
Run from that same Windows client, what is the result of the following commands:
nslookup pi.hole
nslookup flurry.com
The screen shots showed that DNS requests to lookup the hostname MAT wernt working, which is expected. nslookups to pi.hole and bbc.co.uk are working as expected. This isnt an issue with DNS itself more of an annoyance when checking the query log and network table.
nslookup time-outs occur if a DNS resolver isn't responding.
That observation is persistent over all your nslookup results so far, regardless of the DNS server used, and it constitutes an issue independent from the concrete domain.
It may indicate something is interfering with DNS lookups on your network.
I didn't ask to resolve bbc.co.uk - please run the commands as requested.
Also, after running that missing nslookup for flurry.com, please share the output of:
sudo grep flurry.com /var/log/pihole/pihole.log
(run from your Pi-hole machine).
I realised that the windows PC i was running it from has to use a proxy which will block DNS requests. when using a PC not using a proxy it works fine. screen shots are nslookups of MAT, bbc.co.uk (which you didn't ask for) 
and flurry.com. also the logs showing flurry.com
That's much better, and it gives all the expected results.
It also demonstrates that your .3 Pi-hole does know how to resolve local names.
At the same time, it strips us from possible explanations for your observation (unless that proxy would somehow also interfere with that Pi-hole at 192.168.12.3?).
Could you provide a fresh debug token, please?
Your previous one has expired.
Or make that two tokens, one from each of your Pi-holes.
Hi, I seem to have fixed my network table issue. previously I had tried to flush the logs and flush the network table separately. However, over the weekend I decided to flush the logs and network table at the same time. This seems to have resolved my issue as my network table is leaving the hostnames blank for devices it can’t resolve
Thank you for taking the time to assist with this, I really appreciate it.
