These messages you mention are in the boot output of my normally functioning yun so they are not likely to be symptoms or causes of your problem.
- "No valid address in Flash. Using fixed address"
- "Initrd not found or empty - disabling initrd"
- "Error: Driver 'gpio-keys-polled' is already registered, aborting...".
If I run reboot I get the same output as you do just before the reboot:
root@Arduino:/# reboot
root@Arduino:/# [ 485.140000] wlan0: deauthenticating from 00:1c:10:05:e3:9c by local choice (reason=3)
[ 487.170000] Removing MTD device #3 (rootfs_data) with use count 1
[ 487.190000] Res?
U-Boot 1.1.4-gd995931a-dirty (Aug 7 2013 - 16:16:04)
Arduino Yun (ar9331) U-boot
What does your rc.local look like?
It looks like you are not using a wifi connection. Have you disabled wifi-live-or-reset?