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I figured out what was happening. When I made the changes to the Java package to do the uninstall, I published the changes thinking that was enough. After Windows Updates installed the update, I looked in the c:\windows\softwaredistribution folder in the downloads folder. There was the executable for the Java update and the other files in the package. The date modified on the XML file was 2 days ago. I opened the file and none of the changes that I made where there. I published the package again, but this time I chose to delete the package first. This corrected my issue.