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The Preferences are global settings, which are stored in the Windows Registry. So they apply to all games/protocols.
To minimize CPU-usage it may help to minimize FaceTrackNoIR, after you have started the tracker. You can do that manually or set the delay, so FaceTrackNoIR can minimize itself.
It is possible to 'Start' the tracker automatically too (only use this, when you are sure all settings are OK).