Year later still have this issue.
Other similiar thread:
Is there any solution?
When I test it's working on some files but most of the times is not (From the time line screenshot below it didn't make another empty group.)
My original working file doesn't use gradient/masking, just a flat vector.
can you upload the Ai file that's causing you issues? I would like to examine this further.
Hi Roei, thanks for the reply.
I finally found what the problem was!
The problem will appear your object in AI files have opacity below 100%.
You can see here clearly: https://dl.dropboxusercontent.com/u/63499976/shape_convert_folder.zip
Solution: don't make any object in AI transparent before you import to AE.
(repost from other thread)