Robot Restart and Reset Issues

[GeeTwo]

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

Our autonomous code generates several arrays of data during the robotInit method.

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().