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That's ..interesting. I also got a a lot of image consistency errors on our Atlas's SA Camera until I enabled the "packet resend" feature of the Flycapture API. See here for an example of how this option is set.

The symptoms you describe sound somewhat differently (working every other time you start), but these are some other observations I made before enabling the resend option fixed things for me:

High load on the Network caused significantly more image consistency errors.
Increasing the MTU size significantly reduced the number of image consistency errors

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