Personally I don't have this problem with the same camera... Is it the case for any light metering setting? I usually use the partial metering. Trying different meterings might solve the problem, besides bracketing of course. I found this online on this topic: http://photo.net/canon-eos-digital-camera-forum/00ZR2a
Btw. I see you use the 60mm f2.8 macro... Any other way to use it with the 5Dmk2 then with extention tubes?
Is your screen calibrated? My 5DMKII gives great results, I only shoot in RAW and on manual so I complete control of my speed, aperture and ISO. I rarely have blown highlights so something somewhere is going wrong for you.
Canon L 28-300, Canon L 24-70, 50mm prime f/1.4, 2 x Canon 580EX II F...