On the Creating issues and comments from email, it is stated that the incoming processed mails are deleted from the mailbox, regardless if the mailbox type is POP / IMAP:

Note — how JIRA handles messages on a mail server/service:

• For mail accounts, JIRA scans email messages received by your mail account's 'Inbox' folder. However, for IMAP mail servers, you can specify a different folder within your mail account.
• If JIRA successfully processes a message, JIRA deletes the message from your mail account (on a POP or IMAP mail server) or file system (i.e. for file system messages).
• If JIRA does not successfully process a message, the message will remain either in your mail account or on the file system.

This should be corrected as messages are deleted only from the POP mailboxes, while on IMAP mailboxes, these are just marked as read.