I have same problem. I could only see a fraction of my project photos if I browse the Aperture lbrary. It is the same problem when I sync the aperture photos to my iPhone or iPad. I still cannot solve it but I know a way to go around it for your iMovie to see the pictures so that you can work on your iMovie.
Here is the work around:
Export the photos from your album to your hard disk and re-import into your iPhoto. Now you should be able to see those photos that you want to work on in iMovie when you browse your iPhot library.