Well we found our problem on Saturday. It turns out we didn't image the cRIO with the right image. In fact, the programmer never updated the imaging tool like he was supposed to... so no new image, no Black Jaguar plugin, nothing...
After we updated the cRIO, we got a solid amber light on our Jaguar.
Only 1 Jaguar worked though. Turns out the phone cables I bought were reversed. I spliced them this weekend. We never did get them running. I'm sure it's a simple problem. Probably the fact that it couldn't find ID #3, the Jaguar with the wrong cable.