I've through a lot of trouble using my new 6D with my 580EXII on TTL mode.
I used to use the speedlight with my T2i using center weight metering and it worked flawlessly all the time
Now with the 6D, it heavily underexposes at random intensities. I have to set it to +3ev compensation to get usable slightly underexposed images (not perfect but ok to lift on post). some times +3ev over exposes and I have to set +2 or +1.
I used that flash with T2i for 3 years so definitely I'm not commiting any dumb misconception while metering or analysing the situation. I always shot events using center weight metering on T2i and it worked great.
ps: I'm using magic lantern. I'm already using it for about 4 years and I know it may have bugs but now sure if it affects the metering
I think I've experienced what you're talking about to some degree. Can you give me some more details of what shooting settings you were using? When I've had this issue, it's almost always had something to do with the shutter speed. If I work in manual mode while still using ETTL I don't seem to have these issues. For whatever reason it sometimes decides to way underexpose.