Go to Chat Logging Filter (Messenger Plus! Live Preferences panel>Conversations>Chat Logging) Here press on Filter button and make sure everyone is selected for their chats to be logged. Also set the "Default value for unknown or new contacts" option as "Enabled". (I think it is set as "Disabled" on your computer because you said you have ADDED RECENTLY so they are filtered out by default due to that option
The option "Enable chat logging" in Convo window's Plus! menu is to change the preference temporarily without touching the real filter. For example, if you want to say something secret and don't want it to be logged in the log file, then you can easily use that option to disable chat logging for a while without going to the real filter.
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