When you reply to an email, does not goes to that email inbox which you set in POP3 email? Please do the following and let me know.
1. Create a new message
2. Reply to that email which is sent to recipient email address.
3. Check inbox of that email which is set as POP3 email. Does that reply in email inbox? Does that email has message key in email subject? Does that email sender email is same as that user email in your website?
4. Wait 15 minutes. Refresh your website couple of times. Does that email still in inbox of that email address? Is it imported as message in your website?