Any experiences, help or advice would be appreciated.
I'm sorry for asking this, but do you half-press to focus first and then you take the shot? Or do you use a full button press to focus-and-shoot the most quickly possible?
The 6D has a delay that you can notice when using full button presses to take the shot. And that's compared to my XTi. I don't know if that is what you are experiencing. More info: http://www.dpreview.com/forums/post/52069474
Turning off the "Superimposed Display" in C.FnII turns off the red blinking light, and resolves the issue (however you will have to stay without the red light confirmation).