Eu tentaria alterar a configuração de gerenciamento de energia no HDD via hdparm
.
$ hdparm -B <value> /dev/sdx
Detalhes
-B Query/set Advanced Power Management feature, if the drive supports it.
Allow value means aggressive power management and a high value means
better performance. Possible settings range from values 1 through 127
(which permit spin-down), and values 128 through 254 (which do not permit
spin-down). The highest degree of power management is attained with a
setting of 1, and the highest I/O performance with a setting of 254. A
value of 255 tells hdparm to disable Advanced Power Management altogether
on the drive (not all drives support disabling it, but most do).