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Not working

I have the plugin setup correctly, I went in and added my HTML, but all system emails/notifications to users are sending just as before, as plain text with no HTML. Any help would be much appreciated.
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At @rcapell: Can you leave us some version information. That might help.
If i read correctly then "HTML templates" are also in the pipe for the core of 2.3 or 2.4 of Vanilla.