Make sure you are running the latest firmware (1.03 I think) since some people reported issues with the fans turning off on the older ROMs.
The temps you are seeing look fine.
When the drives are not running the blue vertical bar should not be lit. So you might start by assuming that the drives are running (generating heat and keeping the fans running), and see if you can track down a problem with that. I'd start by turning off all of the servers (FTP, UPnP, iTunes, DHCP, etc.), unplugging the unit from the network, and waiting 15 minutes to see if the drives go to standby and the blue vertical light goes off. If that's successful, you can start turning on the servers and seeing which one is causing the drives to stay on. Maybe there's something else in your network that is touching the NAS every now and then, preventing it from going to standby.