Suppose one uses a dedicated query window, receives some messages from someone else, and then opens a query with that person. The other person's messages are then not copied to the query anymore, despite "Copy messages to query" being checked, if "Automatically log" is set to "None". If set to "Chats" or "Both", the messages are copied as expected. I suppose more specific log settings can affect the behaviour, but this is the gist.
