There is no indication that emails are not in the inbox. I just look in
the
unread mail file and find emails there that I know are not in the inbox.
You didn't answer my question. The Unread Mail folder contains the "In
Folder" column that tells you where each message actually resides. Where
does that field say the messages are? If it says "Inbox", then they are in
the Inbox no matter what you believe. The likely cause is that you have a
filtered view in the Inbox that is hiding the messages, but they're still
there.