Instead of using the Settings > Upgrade page on the web UI, you may want to install the software upgrade from a TAR file.
Must have root access to the appliance and be able to transfer a file to the appliance using SCP or the equivalent.
/etc/utils/verify-reboot-upgrade.sh /home/atpsa-version_string-x86_64-DVD.tar
The upgrade process is fully automated at this point. The server will reboot twice before the upgrade is finished.