What F-stop were you shooting at? When I use my 100 L macro I like to shoot at like at least F8 if i am shooting macro. But I will stay 100L macro is a very touchy lens but I have only been using it for a few weeks.
The first time I used the 100 2.8L was about 2 days after I received it. I attached it to the T3i and went over to Filoli mansion: http://www.filoli.org
I used the lens wide open on daffodils and tulips. This past weekend, I stopped it down to f4 and f5.6 -- thinking I should be able to achieve better results. NOT
Sounds like Daffodil Hill. Fun place to shoot.
Perhaps part of the issue is simply DOF difference between crop and full-frame sensors.
Daffodil Hill came up in a conversation I had with a fellow photographer on Saturday at Amador
I actually was thinking along these lines since the results I got with the T3i were so much better.
I have some pics taken with both the T3i and the 5D MKII that I can post later. The differences are quite apparent especially when you consider the T3i/100 2.8L shots are all handheld. To be perfectly honest, I'm ashamed to post the pics from the 5D MKII -- they're that bad.