Ok more news. I figured out the PS3 darkness. There is a Display Settings setting called RGB Full Range (HDMI). I had this set to Full. Changing it to Limited fixed the problem. It's pretty scary because now I wonder if I watched all of my movies in the wrong way all of this time. I found this post that says you should always use Limited. http://www.avsforum.com/t/1351448/ps3-full-rgb-and-white-balance-question

I will have to check a real Blu-Ray and see if it makes any difference. If it does, I will have to rewatch all of my movies to see the improved picture quality. ;-)

I tried a bunch of other settings in After Effects, but VLC always reports 48fps. I will keep playing with it.

Edit: I tried a Blu-Ray (Star Wars Episode IV trench run scene) and the PS3 setting doesn't make any difference that I can see.

Also, my video is encoded as RGB, but Blu-Ray's are encoded as YCBCr so I will try encoding in that format and see what happens. This would explain why the RGB setting makes a difference on my video and not on Blu-Ray's.