Usually 1 IP address is for the website and the other 2 IPs are for the name servers. You have to make changes through your domain control panel.
It should still work though.
Did you set up child hosts at your registrar for ns1/ns2/ns3.yourdomain.com?
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Have you checked that the advanced DNS are configured correctly? you can access the cpanel of each account? try making this:
- Upgrade the cPanel (principal WHM)
- Check that the domains are added in your clients accounts
- Check that the advanced DNS are configured correctly (if not, press on "Restart configuration" in advanced DNS)