If you are using your server for MX record then make sure that you have not enter the domain name in /etc/remotedomains. It will remove all the domains which are listed in /etc/remtedomains from /etc/localdomains if you run fix mailbox permissions from WHM.
The domain listed in /etc/remotedomains should not use your mail server.
Yes, that was the reason. I had removed the domain from /etc/remotedomains and now the issue has not been arised.
Thanks,
Alex
