In the past few months I had a Western Digital USB2 External Drive attached to the USB port of the time capsule - and was copying data to an from it without any problem for a period of two weeks. In the past when I was getting the disconnect popup and repeated 5-minute partial spinup - I was also experience strange behavior with the (same) external WD drive attached to the USB port of the time capsule.
It is my understanding that a USB drive attached to a Time Capsule is not 100% the same (physically) as a USB drive attached to an Airport Extreme - although logically from a use standpoint - the interaction with the device appears to be the same. Apple does specifically state that Time Machine Backup is not supported when the backup destination is a USB drive attached to an Airport Extreme - but it "is" supported on a USB drive attached to a Time Capsule. This would be an indication to me that there is a slight hardware difference. They do say that storing files on a USB drive attached to either a Time Capsule or an Airport Extreme - is supported - just not Time Machine.
In the past I could trigger the disconnect popup as well as the 5-minute partial spinup - by just copying my iTunes library to the TC (at that time it was about 25 gig). The copy would complete successfully - but within a few minutes of completing the copy - the disconnect popup would appear on the Mac used to do the copy - as well as popping up on any other Mac that may have had the TC share mounted at the time - even though the share on the other macs was not being actively used.
When I was trouble shooting this problem a long time ago with Apple - I reverted back to 7.5.2 as well as the 7.5.1 firmware. At first - this seemed to have fixed the problem - but within 24 to 48 hours - the identical behavior would resurface. The behavior was the same on both my original Time Capsule as well as the replacement that apple sent me. It does (or did) appear that something in the process of reverting back to the prior firmware - cleaned out whatever was trigger the problem - but upon re-copying my iTunes library to the TC - I could easily reproduce the problem.
I am now starting to wonder if something in the makup of the data in the iTunes library - at the time - was causing the problem to trigger. As of November - when I upgraded all of my Macs to 10.8.2 and 10.8.3 (recently) - this disconnect popup is very rare - and I have to work very hard to reproduce it. I can no longer cause the 5 minute partial spinup. I did nothing to specifically "fix" this problem. Everything that I am now doing with the Time Capsule - is operationally the same as I was doing when I was having the problem.
I have also never experienced the data share on the Time Capsule truly disconnecting on it own - at least not while it was being actively used. No corruption of data has ever occurred.
I do see anywhere from 1 to 3 reconnect attempts - whenever the Mac wakes from sleep and the share was mounted prior to sleeping - but these reconnect attempts happen in a matter of seconds - and always resolve the connection. To me - this seems like somewhat expected behavior. I also experience the same reconnect AFP messages when I have an AFP share mounted on my Western Digital MyBook Live network drive - although with less frequency than the Time Capsule.
I also wanted to point out - that the Time Capsule has always worked flawlesslessy with Windows - and probably because the connection is done via SMB vs AFP.
I am truly hoping that DJ will report back some of the details that he obtained from Apple a few weeks back.
~Scott