Originally posted by Changelog
Messenger tends to slow down when improper compatibility settings are set for msnmsgr.exe. The setup of Messenger Plus! now resets the compatibility settings set for Messenger in Windows Vista and above.
That's the reason given by the Messenger Plus! Live changelog. I would argue that if it's a big enough reason for the software to do this by default, then it should be used.
Furthermore, if you've been doing it "since day one" then you won't even realise that it's running slow