Comment 8 for bug 1078653

This GRUB_PREFIX line is from an earlier version of grub-common; I removed it in 2.00-1. Therefore, this looks like you had modified /etc/grub.d/05_debian_theme locally, and either (a) you chose to keep your locally-modified version or (b) you weren't prompted for what to do and something defaulted to keeping the locally-modified version. Could you please attach /var/log/apt/term.log so that we can try to tell which of these happened?