Hi JTWhite,
It should work also with normal leds.I personal think you get the best result with ir-leds because you can block al the colors of light and let the ir-light get through.
I use the same cam as you have but I use ir-leds( SFH 485 P)
Did you disable auto-exposure??
You need a tool named windows enabler for it.
Read the manuel how to do it,
http://forum.free-track.net/index.php?showtopic=455
You can also check if maybe you point size of the leds is wrong.
Go to the cam tab, select point-size and give the minimum size a value of 1 and the maximuma value of 50 just for experimenting.
With this funtion you can discriminate other light sources.It is possible that your leds a smaller or bigger so it discriminates them for tracking.
Stormrider