The problem with this approach is that the issue is so intermittent. There's no way of knowing when it's going to happen no way (as far as I know) of precipitating it.
Thanks for the responses guys. To answer your questions:
Eric - I'm not sure exactly what you mean but there's nothing in front of the camera. If I need to I will send it back on warranty but I'd prefer not to have to do that.
Cary - Yes this is the ProRes 422 footage straight out of the atomos
David - I haven't been able to test without the atomos because I only noticed this problem after the shoot. On both occasions it happened towards the beginning of the day, but as a I recall it was very hot. We were shooting in Indonesia with temperatures approaching 100.
I should add that I was recording direct to a Atomos Ninja Blade.