In the span of a couple of days I installed the update to Aperture 3.1 and iLife 11. I've been sharing my library with my wife by storing it on a 2nd hard drive with “ignore ownership” enabled to avoid permissions problems. Everything was working great until yesterday. Suddenly my last project import was acting bizarre and wasn't working when my wife was logged in. The problem eventually made its way back to my log-in. I tried duplicating the images in a 2nd project and it didn't help. And then I couldn't even delete it.
I eventually fixed the problem and it seems obvious now but for the last 16 hours I was stumped. It turns out my “ignore ownership” setting on my 2nd drive had become undone. The symptoms were the result of permission problems. But why? The only thing that seems possible is either Aperture 3.1 upgrade or iLife 11 upgrade somehow changed that setting. It couldn't have been my wife because it requires an administrator password and she doesn't have it.