This is just a piece of mac OSX voodoo: I never use Software Update for a major OS upgrade, I always use the combo installer.
Even though it’s a larger download, the combo updater ends up refreshing a big hunk of your OS so any bits that have rotted get fixed. I’ve also used the combo installer to fix systems that had gotten flaky or wouldn’t boot. So it seems prudent to do in the general case as well.
It’s also much easier for QA departments to test an OS release plus the combo installer. Testing the incremental installer means testing n-1 variants. So occasionally companies find bugs with the incremental but not the combo. In fact, Apple didn’t even make the incrementals available at first.
So if you’re upgrading to 10.6.7 today or even if you’ve already upgraded, you might want to try the combo installer. http://support.apple.com/kb/DL1361