I tried compiling the smartctl from smartmontools 5.39... same effect.
The drive woke up after exiting smartctl.

chr...@bobo:~/tmp/smartmontools-5.39$ sudo hdparm -y /dev/sdb

/dev/sdb:
 issuing standby command
chr...@bobo:~/tmp/smartmontools-5.39$ sudo hdparm -C /dev/sdb

/dev/sdb:
 drive state is:  standby
chr...@bobo:~/tmp/smartmontools-5.39$ sudo hdparm -C /dev/sdb

/dev/sdb:
 drive state is:  standby
chr...@bobo:~/tmp/smartmontools-5.39$ sudo ./smartctl -n standby -a /dev/sdb
smartctl 5.39 2009-12-09 r2995 [x86_64-unknown-linux-gnu] (local build)
Copyright (C) 2002-9 by Bruce Allen, http://smartmontools.sourceforge.net

Device is in STANDBY mode, exit(2)
chr...@bobo:~/tmp/smartmontools-5.39$ sudo hdparm -C /dev/sdb

/dev/sdb:
 drive state is:  active/idle
chr...@bobo:~/tmp/smartmontools-5.39$

-- 
smartctl -n standby wakes up drive
https://bugs.launchpad.net/bugs/497256
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