There are differences in how we detect and list the installed updates. Many updates will be shown as 'Effectively Installed' with Protect - you can include this in your scan by creating a custom patch scan template and checking the include effectively installed box on the general tab of the scan template. You may also want to include the three patch filter types - Security, Non-Security, and Security Tools to match up as closely as possible to what Installed Updates/Windows Update might show.
This article might help explain some differences in detection:
Also, you should upgrade to version 9 at this point. All builds of version 8 will be end of service (no longer receiving XML data) as of May 15.