I took a risk and tried flashing the latest date firmware which is v2.18 (12/21/2011). It looks like the old 2CAN can take this firmware as well. After the firmware update, I can still access the 2CAN dashboard and can see the jags and their data. But unfortunately, the cRIO is still timing out waiting for the Jags to respond. I must be missing something simple.
I have attached the whole code since it is highly likely I missed something in the code.