It's likely your Mac touching files on the drive, especially if you have it mapped to your Finder. I have external drives (one Time Machine, the other just files) attached directly via FW800 and USB, and they'll just spin up randomly while I'm browsing in Safari with no obvious reason. I gave up trying to find the reason.
The only concern I have is the wear on the drives from the incessant on/off cycles, so I think I'm going to just set the option in Preferences --> Energy Saver to disable "Put hard disks to sleep when possible". I'd rather they just spin than constantly cycling.
I'm sure that's no help, but I figured maybe my tale of giving up might give you some peace.
I am having this problem on my 2012 MBP Retina. I have a Time Capsule running 7.6.4 and the only versions available for me to roll back to are 7.6.3 and 7.6.1.
My MacBook Pro will be asleep (Power Nap is enalbed) and my external USB drive plugged up to the Time Capsule will spin up, then immediatly spin down. Over and over again, back to back. It seems to stop when I wake up my MacBook Pro and start using it.
I do have the drive mounted on the desktop before I close the laptop. I would sure like to know what causes this, though, as it's probably killing the life of my external hard drive.