Are you talking in terms of an IMAP expunge command which the settings control, or are you applying a different more general meaning to the word expunge. Like obliterate.

I have 3 IMAP mailboxes, all with the same settings. Two of them perform as expected, mail remains in the mailbox until deleted. One of them has only recently started automatically deleting read emails as soon as the mailbox is closed, without any input from me. The message storage setting Clean Up on Exit is not checked.