1. How are you forcing the drives into standby?
2. Have you reproduced this with a stock kernel.org kernel yet?
One possibility is that these drives may be the kind that
generate a "spurious" interrupt when they spin-down via the timer,
and perhaps libata is "processing" that interrupt and sending
additional command(s) that then wake the drive up again immediately.
To rule this out, you could try using drivers/ide for a moment or two,
and see if the same problem persists with those drives.
You could also try dumping /proc/interrupts in conjunction with "hdparm -S1",
and we can compare that with a "known good" system.
Something like this:
hdparm -B255 /dev/sda
hdparm -S1 /dev/sda
cat /proc/interrupts
sleep 6
cat /proc/interrupts
Cheers
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