600EX-RT output inconsistencies

I am curious if others are having any issues with the output levels on their 600 flashes? Specifically, when using remote lights in Manual and on camera in ETTL? What is happening is that he off camera lights, even if set to a specific output level, are firing at different levels each time. If a 3rd party remote trigger like a pocketwizard is used the output stabilizes a set level though. This is using Gr mode on the Master flash on a 5D Mk3. It just seems like the Master is still transmitting scene information to the off camera lights even though they ought to be locked in to a output setting. I've had 3 people ask me about this happening to them, and I am at a loss as to what's going on.

Thanks!

Eric