You didn't give us much information (such as: Is there a pattern?, all mail or some mail? how you access your email?), but here are some things to think about......
How do you access your email? webmail or email client (Outlook, thunderbird, etc), or mobile device? Do
you have any email clients (pc or mobile based) configured as POP? If so, the client may be downloading the messages and deleting them from the server. You most likely want to reconfigure to IMAP or possibly check an option such as "leave mail on server when downloading" IMAP and POP don't mix well. If any client uses IMAP (which keeps a mail on the server with the intent of email being accessed from multiple locations) then everything should be IMAP. Also webmail is really a web-based IMAP client, meaning that if you are using webmail you are using IMAP.
Is all your email disappearing, or just the oldest email? Is there a pattern? You mentioned mailbox size was unlimited, but have you checked the auto-archive settings located at mailboxes.yourdomain.com ?