The IFI control system can enable the robot before the autonomous flag has been set--this was documented elsewhere, although I cannot remember exactly where.
What I would do is poll the disable and autonomous flags. On the first start of the robot controller, monitor the disable flag--the first time it goes low, even if the auto mode flag is also low, prevent the operator code from executing. Only allow the operator code to execute on the second disable high-to-low transition. (It is guaranteed that the disable flag will go high in-between autonomous and manual control modes)
Hope this helps!
Eldarion
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