When you say "when we put them on Digital O/I 1 we see the lights, but they are solid," I take it you are referring to the IR emitters seen through a camera? The frequency they blink at is too fast to be detected by humans, and a camera's viewfinder refresh rate will make it even more unreconizable. The best way to make sure your beacon is pulsing is to put a visible wavelength LED in parallel with the IR leds (don't forget the appropriate resistor). Shake the beacon back and forth really quickly. If you observe a continuous blur, your IR emitters aren't being pulsed. You should observe a 'strobe effect' - rather than the visible-wavelength LED apearing as a blur, it should apear as a series of dots. If you don't see this, then you're either not sending the right pulse signal (check your wiring) or your wired your transistor up wrong (FIRST origionally released a mistake with the transistor wiring - make sure you didn't wire it according to that document).
Also, there are two different version of receiver.c. I believe the one in edu_tracker.zip is different than the one in tracker.zip - open the file up and make sure your sensors are wired appropriately.
[Edit/Shameless Plug]
I wrote a whitepaper about debugging your IR setup -
http://www.chiefdelphi.com/forums/pa...le&paperid=263
Check it out if you haven't.