To use the 10.6.3 DVD you *must* use NBI 0.8.4 RC1 or later. If you do, it will install without issues.
The 10.6.4 update also applies without any issues (again, tested with 0.8.4 RC1). NBI automatically runs after the update and patches the machine. Afterwards, it works just like before.
One user commented that the new kernel does not change the pm version, and as such, you need to manually specify pmVersion=19 (or =0) if you use SleepEnabler.kext instead of the native power management.