I have had the same problem which I solved in earlier versions of Kubuntu using 
the following script
#!/bin/bash
# exec >/dev/null 2>&1
exec 2>&1
pumount $1 || umount $1
sdparm --command=sync $1
sdparm --command=stop $1

This worked fine until I moved to Jaunty and now it no longer works - sdparm 
seems to do nothing although there is a small 'blip' when the stop command is 
executed so maybe, as others mentioned, the drive does stop and then restarts 
again.
I am using a WD drive (maybe as passport, I bought it some time ago and it just 
has WD printed on it). There are a couple of ext3 partitions only on it.
This has been a long standing issue and it is worrying that it may result in 
hardware damage and/or data loss but it is only set at a low priority.
Please raise the priority of this issue
Thanks

-- 
WD external drives need to be spun down, "sdparm --command=stop" doesn't work 
any more
https://bugs.launchpad.net/bugs/117713
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