Originally Posted by yancek
What are you updating?
If you are running update-grub, that would be expected behavior.
I'm not sure if I'm reading that the way you meant but I take that to mean when you update-grub on the SD card, it updates and changes the bootloader on an internal hard drive, is that what you meant? That's completely illogical. I have Ubuntu on sda5 and I can run update-grub on it and it will add any new systems to the grub.cfg file in Ubuntu but has no effect on the primary system on another partition which has Grub in the mbr which is also expected behavior.
It happened when I did a dist-upgrade, and I think that several packages that updated the initrd were updated, along with grub. Maybe the the latter happened (your interpretation is correct) and it added the fixed disks to the SD card's configuration files. I don't want that to happen.
It may be that I can experiment with it a bit more to see exactly what happens to the system, but I definitely don't want it adding fixed disks to the bootable sd card's boot menu. I think the last time it did, it wouldn't boot when the card was put in another machine.