The problem is easy to reproduce, but it takes time to do so. If I set a POP client to download from the mailbox every 5 minutes, within 12 hours I will download a batch of messages that are from about 10 months ago (sometimes in that 12 hours, I'll get 5+ copies of the messages). I can reproduce this on any PC, any OS, any Client (and yes, on clients that have never before logged into the mailbox). Additionally, I can get the messages to show up in the ISP's Horde web client but I have to be watching it because on the next refresh of the mailbox, they are gone. It seems like the client, web or POP, has to hit the mailbox at just the right time to get the messages.
Does Qmail use a mailbox or inbox file that can be deleted if corrupted and then recreated?