Just out of curiosity, does After Effects also see it as 30 instead of 60? (I will take the shortcut of 30 instead of 29.97, etc throughout this post.)
I understand your desire to shoot 60 and edit at 24 because I do that a lot.
If you put the footage on a 60 fps sequence, and go through it frame by frame, does it repeat frames in order to play it back at the correct 100% speed?
Could you shoot a 5 second clip and post it to where we could take a look at it and see what happens on our systems?