Scenario

User experience this with after receiving an e-mail for service desk.User is are able to see the incoming mail in the mail box for a few seconds. The e-mail is then processed via POP from Jira and is no more visible in the mail box. 

Workaround

To resolve this issue we changed the email settings to IMAP and the issue stop occurring after that.

Here is how you can configure the email settings : Configuring JIRA to Receive Email from a POP or IMAP Mail Server