How is your workflow set up? How are you moving the Aperture Library around? What OS X and what Aperture versions?
After backup to an independent drive (stuff happens...) make sure all apps and the OS are current. Also read this regarding
Perhaps my issue lies between the OSX maybe. I am using Leopard on my MBP and my iMac has Snowleopard. Lion was just coming out when I got my machine but wasn't installed on it and frankly I forgot to even install it after the fact. I will try to re-create the error screen and provide a screen shot as well. As for everything else, it's all up to date and I am using the latest version of Aperture 3 as well.