Can you give us some more details? Where are the lights that you are seeing?
Is this the first time you've hooked up the cRIO? Was it working previously?
Have you already been through the bench tests suggested in the FRC Control System Manual (chapter 2)? If not, take a look, particularly at Chapter 2 Getting Started:
Control System Manual
http://www.usfirst.org/community/frc....aspx?id=10934