Have you checked your footage interpretation and your comp framerates in the project settings? That's always the first place to look. In your case you might also want to check pulldown/ fields. I think CS6 has changed some things for reverse pulldown footage as it is produced by some cameras that use 60fps to mimic 24p. If you provide more details, people will be able to help you better than just guessing around...
How long is my piece of string?
Can you please provide a screenshot or two showing your frame rates and how you are interpreting your footage, etc?
A picture is worth 4000 words....
thanks for the quick help. all comps settings and footage interpretations are like in cs5.5. but i found the issue. it has something to do with the little sun you can turn on/off for precomps. i think it's called collapse transformation. when i turn it off it looks like it should be and when i turn it on it looks different. but in the original cs5.5 project it was turned on because of the different blend modi i used in the precomp. so i don't know really what to do? and why is that anyway?
To figure out what is going on we need to see a screenshot of your comp with the layers and blend modes. We also need to see a shot of the pre-comp that is giving you problems.
Also, confirm the exact version number of your application. (I.e., have you installed the most recent updates and are running After Effects 11.0.2?)
In general, it helps if you provide answers to the questions listed here: "FAQ: What information should I provide when asking a question on this forum?"