[RufflesRidge]

Running with Front Panels open can significantly affect the CPU Usage an consequently the timing of your VIs. When combined with usage of the CAN Bus, running from the PC may be causing CAN timeouts. These timeouts trigger errors which are computationally expensive to process, leading to more errors resulting in never being able to communicate with your Jags.

Just a theory, but I would check the Diagnostics tab of the DS and the cRIO CPU Usage on the Charts tab in addition to the NetConsole suggested above.