I was testing the mail client in M18 and I selected "Leaves messages on server" in my POP mail server settings. However, when I "Get new messages", the messages are deleted from the server anyway.
Does shutdown then relaunch fix it for you? I wonder we may not refresh the pref after checking leave message on server option.
Apparently, I just discovered a "feature" of my ISP's mail system. Your mail is deleted when you pull it regardless of what the client says. I tested mozilla M18 with my other two mail accounts and the "leave message on server" functionality works correctly with those mail servers. Sorry for the inconvenience.
Thanks for double check with other servers. Mark it verified.