I upgraded to cs6 and imported all the images together, I made them 3 frames per and exported them. The problem is slightly improved but still there. I'm still getting flicker.
Check it out: http://www.youtube.com/watch?v=g_yZjskzTLs
Black screen version from yesterday if you want to look at it: http://www.youtube.com/watch?v=NCcAEO8YU6Y
The problem has to be with my settings. when I upgraded it deleted all my prefrences and settings. There was no dslr preset either so I had to redo it all from scratch to the best of my ability. Here is a complete rundown of my settings:
I shoot with a canon dslr 60D in 24fps and upload all my stuff in 1080p. Please advice.