did you change any defaults in /etc/freebsd-update.conf?
What exactly was the command you executed?
With root you mean / or /root?
You really need to provide more information. I'm not a freebsd-update pro myself, but the guys with more knowledge will surely help if you put a little more effort into a god question with enough information
I've seen this happen before. Are you dual booting with Linux and use Grub to boot FreeBSD? It's a setting in Grub that causes the freebsd-update(8) script to use the wrong data and you end up with almost everything in /boot/kernel.old. I need to search for the thread but it's been covered before.