Not sure if this is helpful but I did some playing and I wonder if this
has something to do with how grub-pc interacts with startupmanager. When
I try to install startupmanager on a machine with grub-pc:

la...@lance-desktop:~$ sudo apt-get install startupmanager
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following extra packages will be installed:
  grub
Suggested packages:
  grub-doc mdadm
The following packages will be REMOVED:
  grub-pc
The following NEW packages will be installed:
  grub startupmanager
0 upgraded, 2 newly installed, 1 to remove and 0 not upgraded.
Need to get 0B/525kB of archives.
After this operation, 201kB of additional disk space will be used.
Do you want to continue [Y/n]? n
Abort.

Of course I don't know if all the machines effected had startupmanager
installed or not. Just a thought.

-- 
apt wants to remove grub2 for machines that did upgrade legacy grub
https://bugs.launchpad.net/bugs/445653
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