Did you get the 14 MB update for 10.3.6, or was it the larger 34 MB. I suggest going to Apple's website, get the full package, and install it. Then Repair Permissions, and also get something like MacJanitor, to run the cron jobs.
Oh, and BTW, it shouldn't have anything to do with the installer size, as SU checks what you need and only installs these AFAIK. That's why there are different sizes.