Here's another issue I got from both Clifton Hughes in our Irving, Texas office and Keith Thornley out in North Carolina. We're starting to see this somewhat frequently so hopefully this will help you avoid a potential headache:
Issue: After applying the MSXML3 SP10 update released under KB955069, ScanWrapper fails to run and ScanWrapper.log will show the following error:
Unable to upgrade the existing MSXML3 component on the machine. Previous version is protected by the OS.
Unable to install correct version of MSXML. Upgrade to latest version of MSXML3 and re-run scan. This is terminal error.
You may also notice that updates will install, however the status for the clients may show Pending Reboot, rather than installed.
Cause: This problem occurs because the program checks to see if MSXML 3 SP2 (version 8.20.8730.1) is in place before running the scan and ScanWrapper.exe compares the current version of MSXML3.dll (SP10 is 8.100.1048.0) with the 8.20.8730.1 value and mistakenly thinks SP10 is older than SP2.
Resolution: You can work around the problem by adding the /noxml switch to the command line for the scan programs in the SMS Admin Console. In addition, both Command1 and Command2 entries in the Scan.ini file for each package need to have /noxml added. Just be sure to update your DPs once this is done.
J.C. Hornbeck | Manageability Knowledge Engineer