A number of people have mentioned not being able to update to OS X 10.6.5, especially when they have used the standalone Combo updaters that have been found at sites like MacUpdate. After installing these updates, they have found the system still to be running OS X 10.6.4.
When the OS X 10.6.5 update came out it first was only available via Software Update; even if Software Update sites had the standalone Combo and Delta updaters available, they likely linked to prior versions of OS X. These Web sites host legitimate software, so it is very likely no harm was done and only a reinstall of the current OS was performed.
Your best bet in this situation is to use a source for the download that comes directly from Apple, or ensure the software site is hosting the latest version of the OS before downloading and applying it. If you are unsure, either go with Software Update to install the latest OS version, or download the updates by clicking the download links in the following Apple-hosted Web pages, Mac OS X v10.6.5 "Delta" Update (644.48MB); Mac OS X v10.6.5 "Combo" Update (977.21MB).
If you have OS X 10.6.4 on your system, then either of these downloads will do, but if you have a version prior to OS X 10.6.4 then you will need to use the Combo updater or use Software Update. We recommend using the Combo updater, and you might consider booting your system into Safe Mode before installing it to avoid any potential interference by third-party plug-ins and log-in items.
If the update still does not work, then try performing a general system maintenance routine before rebooting into Safe Mode and applying the Combo updater.