Generally speaking, the automatic software update feature of OS X is pretty good. That being said, there are times when running those incremental updates just don’t seem to work quite right… due to who knows what.
Fortunately, Apple almost always combines all the recent updates in to one package, and makes them available for download.
If after an update (through Software Update), your computer seems to be behaving strangely, or you start having a problem that you didn’t have before the update, it may be a good idea to download and install the combined updater. Doing that can sometimes fix little problems. The current combined updater is 10.4.5, and can be downloaded here.
One more tip… whether you are updating through Software Update or downloading the standalone combo updater, it’s always a good idea to repair permissions before and after and major software installation. You do this with Apple’s Disk Utility, located in your Utilities folder.