The most likely thing to cause this sort of behavior is if some piece of hardware (probably a sensor) other than the 'RIO needs a few hundred milliseconds to initialize. Once this initialization is done, the 'RIO initialization works.
Have you tried inspecting your 10MB data block to see what is different between a successful and a jerky startup?
Also you indicated that
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Our autonomous code generates several arrays of data during the robotInit method.
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If this data is only used for autonomous, and you can spare the half second, try moving this array generation to the beginning of autonomousInit() rather than robotInit().