Focus problems with 60D and 100-400mm?

Hi, I recently upgraded to the 60D from the 40D because I wanted to start doing some video. However, I seem to have possibly run into a problem. The AF on the 60D definitely feels quicker than with the 40D however when doing some bird photography this morning with my 100-400 I was finding that the AF didn't seem to be as accurate as my 40D. I would get the red AF confirm box but when I zoomed in on the preview it appeared slightly of focus. Some of them seemed better than others but most of them seemed slightly off. Has anyone else with the 60D had this problem? Is it just that the 18mp of the 60D is out resolving the lens and the slight out of focus is just the effect of the extra megapixels magnifying imperfections that the 40D couldn't see? Or should my 18 megapixel images appear almost as sharp on the 60D as they did on the 40D at 100%? I think I might go do a test after this and compare the autofocus to manual focus using live view and see if there is a big difference.

Is it just that the 18mp of the 60D is out resolving the lens and the slight out of focus is just the effect of the extra megapixels magnifying imperfections that the 40D couldn't see?

I think that's one factor, definitely. The 100-400mm isn't the sharpest knife in the drawer so you may be feeling that. One thing that WOULD have helped is if Canon kept the backfocus adjustment in the 60D. I don't understand why it was in the 50D then taken away, quite odd. There is one way to get it as sharp as it can be, but it's not fun: set up a repair order with Canon and send them the lens AND the body and they will adjust it for you. It could be the lens needs a tweak or even the body, but that would at least get you to the best possible place, frustrating as that is to ship your stuff away. Because the 60D is under warranty it is VERY likely they won't charge you to adjust the lens, especially if you send it to Riverside, CA.

I have 40D too and I find 40D slower than my previous 450D in autofocusing but the autofocusing is dead accurate. I am not sure about 60D. At least I have not seen any such complaints. I don't think the resolution is an issue, because couple of my friends are using 100-400 on 7D (18 MP) and are getting crisp pictures with stunning level of details. Hence you should not worry about it.

Hmm...I think I'll need to perform a test by autofocusing and then using live view to focus manually on several different test subjects to eliminate the possibility that I just chose a subject that is difficult for AF in General. If the manual focus seems to be significantly sharper then I'll assume the AF is off but if its pretty close I'll assume its the normal margin of error because manual focus is always going to be a little more accurate. I might try it with my other lenses also and see if I just didn't notice it on them because I'm not cropping with them like I am for wildlife with the 100-400 (that way I wouldn't have to pay to ship the lens too).

Its is pretty dumb that they left the micro-adjustments feature out of the 60D when they had it in the 50D. They made some great improvements in the 60D but they also made some mistakes with the parts that they dumbed down. Shouldn't they have seen it as a feature that could potentially save them money on having to repair peoples slightly off AF....or maybe they saw it as a way to make money if people don't do anything about it until after it is out of warranty?