Just a guess
It will also fire up if you do something on the Mac that requires all the drives to be available. Something like a Save As command, for instance.
I have a 500GB LaCie external HD, about two years old, with two partitions. It continually fires itself up (whirring noise as if transferring) and off every 5-10 seconds. Oddly, when I demount it, the problem goes away. presumably it's not just the HD - something on the Mac is winding it up. Any ideas?