I kinda had a similar problem. I had 7 layers of video on my sequence with heavy time remapping and cropping. And when I exported the file, only the first layer showed. When I’d go back to FCP, only the first layer was showing. And then when I’d click on the “hide layer” button of one of the tracks, they would all suddenly reappear, but I’d re-export and nothing would show but the first layer. I tried copy-pasting into another sequence and into another project, I tried deleting the preferences, repair permissions, heck I even unistalled and reinstalled Final Cut Studio! Nothing would work..
Then I started switching off effects and such, and I found out that when I reset the crop fonction, the layers would export correctly again.. Wich was a bummer, I needed the crop!. What I did was to export each layer separately, and crop them in a new sequence. I don’t know what was happening, but somehow the file was corrupted along the way, and the crop function was causing problems only in that particular project.
Any who… Switch things on and off and hope for the best.
Cheers