So we have a SMC SY3000 series solenoid wired to ports 1 and 2 on the cRio. There is only one red light lit at a time, and when we press the trigger, it changes to the other one. The problem is that the pneumatic that we have attached to it doesn’t fire. We have checked pushing the orange buttons on the solenoid, and that works just fine. What are we doing wrong?
I’d check this out and double check your set up: http://www.team358.org/files/pneumatic/ great resource by Mark and team 358 
Are you using a 24v or 12v solenoid and where is the Solenoid Bumper getting it’s power from (12v or 24v)?
12v Solenoid, 12v Bumper.
How about the tube plumbing?
Are the ports labeled?
Try connecting only the pressurized input line and identify the port it’s connected to.
Is the valve closed?
Are there any leaks?
Is there enough pressure in the tubes to push the piston?
Are you make sure to flip both valves? You need to open one valve and then after a slight delay close the other, in order to change the position of your cylinder.