I use Jaunty, but I installed kernel and hdparm package from Karmic and I still 
have the problem.
Actually, I have 2 disks (let's A, the system one, and B the unmounted one). 
When I do "hdparm -Y" on A, A spins down (but power on just after since it's 
the system disk): this behaviour is OK. But, when I do "hdparm -Y" on B: the 
disk doesn't spin down at all. This behaviour is not ok.I also noticed that 
exactly one every other time I do hdparm, this append to the kern.log:
Oct  3 09:29:28 clairmont kernel: [  674.563643] ata1.00: exception Emask 0x0 
SAct 0x0 SErr 0x0 action 0x6
Oct  3 09:29:28 clairmont kernel: [  674.563654] ata1.00: waking up from sleep
Oct  3 09:29:28 clairmont kernel: [  674.563667] ata1: hard resetting link
Oct  3 09:29:28 clairmont kernel: [  675.090046] ata1: SATA link up 3.0 Gbps 
(SStatus 123 SControl 300)
Oct  3 09:29:28 clairmont kernel: [  675.102961] ata1.00: configured for 
UDMA/133
Oct  3 09:29:28 clairmont kernel: [  675.103006] ata1: EH complete

It changes anything if I swapped the SATA cables, if I select AHCI or
IDE in bios. I think the problem is with the HDD, not with the
motherboard.

Infos:
IDE interface: nVidia Corporation MCP79 SATA Controller (it's a ION platform)
disk A: ST9160821AS
disk B: SAMSUNG HD154UI (<-- the one which doesn't work)
kernel= 2.6.31-11-generic #38-Ubuntu SMP Fri Oct 2 11:06:40 UTC 2009 x86_64
hdparm= 9.15-1ubuntu3

-- 
hdparm -Y does not work (as it did in 8.10)
https://bugs.launchpad.net/bugs/374287
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