[kamocat]

Perhaps your Jaguar is powering up after it is supposed to be initialized, and thus missing the "voltage mode enable" command in Begin.vi. This can happen in systems with low battery voltage or noisy power supplies.

To test this, you can place a "get output" VI and see what output your Jaguar says it's getting. If it's not enabled, it will say its output is zero.
(This differs from the "output voltage" status in that this will change depending on the control mode the Jaguar is in, whereas the "output voltage" will always give you the voltage provided at the motor terminals)