Random question: how are you suspending the device? Because setting up an rtc wake is all well and good, but it's kind of a moot point if the device never actually suspends ^^.
EDIT: Err, duh. Via the rtcwake tool. Never ask questions at 6AM.
.
Still, it's worth checking if it actually suspends properly, and/or whether whatever the Kindle does on its own matches that.
(i.e., there's probably a powerd lipc prop to enter suspend).