That is odd. Gotta think about it. Can you post some shots?
Unfortunately I always deleted them right away and set the correct camera ec, but next time I experience this problem I'll post them here.
You have a good system... 60D and 600EX are good products... although the newest cameras now have rgb metering which reduces auto and TTL flux lots.. its still not perfect.
Thanks for everybody's answers, and yes - my system is very good, after all afaik only the 1dx series has rgb metering (and of course cheaper Nikons, doh). That's why I'm so spoiled and expect my system to work all the time. And for bounce/fill near-macro shots and outdoors fill flash it usually works very reliable, though I have to fiddle with both ec values a bit to get what I want - but in comparison to full m flash this is of course extremely convenient.
But as written above I'll start shooting full camera m more often, just bought the Syl Arena book and will experiment with m flash more often - it's a lot to learn when coming from the "p&s" av+ettl2-experience, but I acknowledge it's more reliable in changing light or with reflecting surfaces, so I have to know how to do it.