Like @lepaapl I upgraded to 7.6.3, and for the first 24 hours it seemed as if Apple had actually fixed this. Alas, after a day the spin-up-and-immediate-spin-down-every-5-minutes-or-so issue returned.
In my case, the problem is limited to my MacBook being awake. When the MacBook is asleep, TimeCapsule stays quiet, too. I can't remeber if this had been the case with earlier firmware versions and I can't be bothered to try. I will go back to 7.5.2. I will go directly to 7.5.2. I will not pass Go and will not collect $200 ...
Update: It's been about a week since I upgraded my 2nd gen extreme from 7.5.2 to 7.6.3, so far the spin up/down issues has not returned. Also as a test I left three macs connected for day to the USB drive; one running latest version of snow leopard, one with the latest lion, and one with latest mountain lion. The only issue I've had with 7.6.3 is with the settings migrated from 7.5.2 for the 5GHz radio mode. 5GHz would not work until I reset/saved the channel settings (In my case from static to automatic).
Just adding another data point to the thread:
Airport Extreme 802.11n (5th Generation)
Buffalo Drivestation Duo connected via USB (configured to back up via Time Capsule)
Running firmware 7.6.3 with an '09 Macbook (10.6.8) and a '12 Macbook Air (10.7.5)
* only had spin up/ down issues when '09 Macbook was awake on the network
* would happen exactly every 2 minutes
Downgraded to firmware 7.5.2
* so far no spin up/ down issues...
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.