Unified Inbox in Mail does not display all emails
My guess is that one of your clients is removing emails from the server - last time I used POP this was the default, and it was one of the best reasons for switching to IMAP. If any of your clients is doing this then those emails will not be appearing on your other clients. Have you checked this on each client that you access those servers with?

I know you didn't say you access those emails from multiple places but it's a common thing to do.