I made an example showing the effects in my video: (normal left, bug right)

I decided to find the cause of this bug and while looking for answers I discovered a solution to the bug, so I made it in to an easy to follow list guide that I will post here for others to use in their project.
1. Export your Quicktime movie with H.264 codec.
2. Open in Quicktime Pro and press ctrl + J to bring up 'Movie Properties'.
3. Highlight the video track then click on the 'Visual Settings' tab.
4. Look for 'Transparency', and select 'Blend' from the drop down menu.
5. Move the slider to 100%.
6. Choose 'Straight Alpha' from the same drop down menu.
7. Save your video.
I have also searched high and low for a solution to the "washed out" look. After an almost sleepless night I came across the fix without having to mess around with color profiles. I'm working from a PC so some of the commands might be slightly different.
After you create the QuickTime/h.264 file, open it up in QuickTime and select "Show Movie Properties." Highlight the video track then click on the "Visual Settings" tab. Towards the bottom left you should see "Transparency" with a drop-down box next to it. Select "Blend" from the menu then move the "Transparency Level" slider to 100%. Right after that, choose "Straight Alpha" from the same drop-down and close the properties window. AND finally, "Save."
So far, it's worked like a charm for me; hope it does the same for you.
Source: http://www.macosxhints.com/comment.php?mode=view&cid=83325