Thanks for the info. But The solutions provided did not help much. Encoding with the x264 codec does not seems to work and changing or adjusting the transparency mode on the quicktime player movie properties works fine but only to view it on quicktime. Once you upload the video to a video share site it will look again washed out. Also if you view it on the VLC player.
After trying a lot I found that exporting the movie as h264 directly from AE, using the H264 format preset, gives much better results and no washed out picture. The trick is selecting the format preset H264 and not using the quicktime format options to change the codec to h264 from there (and AE will warn you). I dont know what really happens but I think AE will encode the movie using another encoder than quicktime and this will result in a better h264 movie, since the gamma shift problem is a bug of quicktime. Exporting from quicktime pro or compressor always gives washed out picture, at least in my case.
I Hope this helps and thanks again.
Manuel F. Rugeles
Editing and Motion Graphics
https://www.youtube.com/user/manuelfeliperugeles