I did the following to update my Mini 9 to 10.6.3
1. Updated my NBI to .8.4RC1 on my working 10.6.2 install.
2. Rebooted without trouble.
3. Repaired permissions.
4. Rebooted again just to be sure.
5. Updated to 10.6.3 via Software Update Here's where I did something different
6. I booted into a 10.6.2 installation I had on a USB key and then
ran NBI .8.4RC1 against the SSD
7. Shut Down
8. Removed USB key.
9. Booted up and it went into 10.6.3 after about 20 seconds.
10. Repaired permissions.
I booted into the USB key and ran NBI from there since it seemed to me
that most issues appeared to be related to rebooting and NBI running for
a long time.
I have since upgraded the USB key to 10.6.3 using the same procedure and
it works great also.