If you can hear the drives "seeking" then something is accessing them - either an external process, via the network or an internal process.
Start by disconnecting the network cable - if this allows it to hibernate, it's an external process, follow it up by check the internal servers - ftp, uPnP, iTunes, etc.
I had a similar situation when I went from 1.05 to 1.06, and it turned out to be one of the internal server processes - there was no repeat when I went to 1.07