Your description doesn't give much detail to work with. I'm guessing that you may be clearing messages via POP3? If so, CiviCRM might be deleting messages which it can't handle? When using IMAP, CiviCRM should move messages which it doesn't understand to a separate folder. Over POP3 CiviCRM might instead delete the message.
The most likely cause(s) for CiviCRM to not know how to handle bounce messages might be:
- your mailings do not contain VERP data, or
- your mail system strips this information, or
- your CiviMail configuration doesn't read this correctly.
But those are guesses; you are likely to get a much better reply if you increase the level of detail in your question. When reaching out for support, you'll improve your chance of successful request if you provide as many variables and as much data you can, eg:
- How is your bounce mailbox configured (POP or IMAP? Is it on a flaky dialup connection to head office?)
- What is the To: address of a bounce message? What do the headers of an email in the bounce mailbox look like before it's deleted?
- What mail server are you using? This shouldn't be a factor, but it shouldn't hurt to include the information.
- Anything else that we don't know about your situation? (Assuming the tool works for the majority of installs, you probably need to describe what might be special about your install.)
Often, taking time to gather this and similar information will lead you to solve the problem on your own. A couple of good reads on this topic: How do I ask a good question?How do I ask a good question? and How to report bugs effectively. Hope this advice will help you move towards a solution!