I'm currently trying to reproduce this problem in a KVM VM. As long, as

#GRUB_TERMINAL=console

line is hashed, everything behaves as reported.
Uncommenting this line and running 

update-grub

seems to fix the problem.

To summarize: if grub graphic console is enabled, one can only boot from
the first HDD.

I'll test it tomorrow on a physical server.

-- 
grub2 installed on raid1 can not boot from second disk when first disk is 
removed
https://bugs.launchpad.net/bugs/594202
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