In all your four cases it is laptop_mode that is calling hdparm (two from 
S99laptop-mode and two from pm-powersave). Can you please add:
 echo "arguments: $*" >> /tmp/pstree.$$
to your "test" hdparm so that we can verify it is changing the -B setting?

-- 
harddrive spins down when it shouldn't in laptop-mode
https://bugs.launchpad.net/bugs/286846
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