Try checking the following:
- MX Entries are stored in the cPanel account for the remote mail provider
- "Always accept mail locally even if the primary mx does not point to this server" is unchecked
There is also a tweak setting "Automatically setup /etc/localdomains, /etc/remotedomains, /etc/secondarymx based on where the mx entry is pointed" but as long as the MX is pointed to a remote domain (e.g. something.googlemail.com) rather than the domain itself (e.g. mx1.example.com) this should be functioning correctly.
If everything looks okay but these issues persist, I recommend letting our technical analysts take a look at things to see what is causing this issue:
http://tickets.cPanel.net/submit