I don't know that much about the base robot code templates for LabVIEW, but I've helped a number of C++-using teams this year who had a problem similar to this, pretty much only on the field and even then, intermittently.
In most cases, they were creating objects that used hardware resources in autonomous (enabled) mode and not cleaning them up (and re-initializing if needed) until teleoperated.
Most of the time this works fine because the field will do the published set of state transitions (auto dis->auto en->tele dis->tele en).
But, depending on various conditions, the control system will sometimes get sent in the sequence auto enabled->auto disabled->{match start}auto enabled->tele dis->tele en. The first 'auto enabled' is very brief and usually imperceptible with regards to actual robot movement. However, it is long enough for the autonomous execution to begin on the cRio.
Cleaning up resources on EXIT of autonomous allows for safe re-allocation if the robot is sent back into autonomous.
This wasn't just a problem with resource allocation -- lack of resetting autonomous state machines, etc were also problematic.
Anyway, my suggestion is to check that the victor and encoder creation (if that's the right LabView term

) are handled correctly if you end up doing auto enabled->auto disabled->auto enabled set of transitions.