Hello silenthunter
1st advantage :
For Freetrack to work, you need to get in the freetrack cam window a high contrast image in which only the markers are visible on a black (or red if you use I420) background.
This is much easier achieved by using IR leds and putting a kind a visible light filter in front of your webcam.
2nd advantage :
With IR leds , you can't get led beam reflections on your screen (really disturbing IMO when you use standard leds, ie red leds), or to be more accurate , you can't see the beam reflections
.
Cya