Folks,
I ran into the same issue (I named it "transparent green screen", I hadn't a better name).
I spent about a week to solve this problem, since I needed it to build a marriage slideshow.
The tools & Config:
iMovie 09, iPhoto 09, Adobe After Effects CS4
Mac OS X 10.6.2, MacBook Pro 13" 2.26 Ghz Intel Core 2 Duo, 2 GB RAM
The Solution for the "transparent green screen":
I created a movie in AE, and put a green background into it. It was the pure green color.
When I imported the movie into iMovie I just got the "transparent green screen", not the real effect.
I some cases, by changing the background images, I could get the green screen to work, but it was kind of random. Which made it harder to solve it.
I thought it could be because of AE, some incompatibility. I went to Youtube and downloaded a green screen video (a woman dancing in a green background). I inserted the video into iMovie, and it worked just fine, all the way.
Then I tried to match the green color I was creating digitally with the Youtube video's green color. It didn't work either. The "transparent" effect was there again.
But when I looked at that Youtube video, I noticed that the green color was not pure. Because that green background was made in the real world, it was not pure, there were some shades of green.
Well, I just replicated that into the digital world. Modified my video's digital green background. From pure green to a gradient green, but very subtle, almost imperceptible. Just to replicate the "imperfection from the real world".
That was it. Solved. Maybe iMovie 09 needs that imperfection to work well. Using "pure greens" might confuses it.
Please do your tests. And let me know your results.
Regards and greetings from Brazil.