Deleting the PLIST file made things worse for me. I'm running 10.7.2.
Whether it was the direct cause or not, after deleting the PLIST file, my files began to all reset their crops to the incorrect way they were looking during export. I noticed that exported images were not matching the crops I have defined, which led me to this discussion thread.
I immediately quit Aperture to stop this, as I have 160,000 files in my library, and the last thing I want is for them to all have their crops set incorrectly!
Another odd thing I noticed was that the files that had been rotated show the image rotated without the edges cropped parallel and perpendicular to the screen. This is the first time I've ever seen this in Aperture. Normally, a rotated image will auto crop to fill the image to keep its edges square to the screen.