Users may find that using Software Update to install Aperture 3.1 fails to upgrade the software. Similarly, attempting to use the manual update (found on CNET's Downloads site) also fails to install the update.
Should you experience this issue on your Mac, you may need to install the latest ProKit for Leopard update, version 5.1. ProKit addresses various interface and compatibility issues for Apple's professional software suites, including Aperture, Final Cut Studio, Logic Studio, and others.
After installing the ProKit update, Software Update should be able to install the Aperture 3.1 update. If you have already downloaded the manual update, you can use that as well.