[Mark McLeod]

MJ, in the instances where the code fails to run on reboot, are there any other symptoms?
In addition to the Jaguars indicating no PWM communication, is the DS status and the robot status LED on the Digital Sidecar indicating good communications?

As an additional diagnostic you might use Wind River to display the processes that are running on the cRIO.

If the DS/cRIO communication checks out okay and you believe the Jaguars alone are having a problem you should be able to verify by adding code that returns a status to confirm it's running. For instance, blinking one of the solenoid module LEDs, like a heartbeat. The PWM cables and their contacts are a potential source of error for the Jaguars.

I've encountered one team here reporting similar symptoms, however, it appears to be isolated to their bridge as the problem disappeared when they reconnected the DS/cRIO directly. thereby eliminating the router/bridge.
I'm meeting with them tomorrow night to finish diagnosing that particular problem.