The custom name that is used in the conversation window is used in the log files. If you use the new Attach original name option, the original name will not be used in a conversation and therefore not in log files.
If you use the (!N) tag in your custom names instead of the attach option, you will see the original name in conversation windows and log files as well. I don't think you can choose not to use the original names in a conversation window while you do use it in the log files.
If this is not what you meant, please be more clear