Can your website run cron?
Please follow step by step
1. Send a message from UserA to UserB.
2. Access UserB email and see if he received email notification. If yes, does that email subject contain [MESSAGE KEY-XXXXXX] ?
3. Reply to that email.
4. Access to your email address (which email you setup in POP3), Did you receive that email which is sent from UserB email ?
5. Wait at least 15 minutes then refresh your website couple of times.
6. Check if replied email from UserB imported in messagebox of UserA?
If any steps failed, let me know which steps it is.
If only step-6 failed, please go to class-fep-email-pop3.php and remove all
error_log and again start from step-1 and after finishing all steps see your server error log and see any error there.
Let me know.