Using a VPS is generally a nightmare to those who have a very little knowledge about it. On this if the emails hosted do not work, that may lead to the nightmare.

We just had the same experience. Emails from the VPS hosted domains were not going to the same domain. So if We have https://www.mydomain.com , and I configure emails to its server say contact@mydomain.com they will not point to the same unless we set (or edit in a later stage) the MX records. While setting up a new account in WHM, by default the emails are set to local mail exchanger. If we have more than one domain on the same server, the emails usually transact between the local and the default settings.  If they do, you probably have a chance to not receive an email on the server.

To get out of this, you can log in to WHM, go to edit MX entries, switch to remote mail exchanger and update the entries of your emails.  Like for my case it was google MX records