It feels like this may got introduced by 1.99-20ubuntu1. And maybe the GPT partition is not the causing factor. My setup uses normal DOS partition table but I use a 2 stage boot where the first boot loader is in the MBR and then boots secondary grub stages from extended partitions. The installation was successful and on previous upgrade I did not notice anything wrong. But the upgrade today produced the "error: non-sector-aligned data is found in the core file" message. The common point is both cases use the deprecated blocklists.
In my case, luckily the system can be booted still. But there is an error on boot saying something about "outside partition" which has to be overridden by typing enter.