Java autoupdates screwing with my Norton scans???

A cpl wks ago began to get Java "just check" auto update alerts.  My nephew said AOK, so I let them come in.  Each time the Java update also comes with an unwanted "free offer" of McAfee scan, I might add.  I say no to the McAfee (of course) and allow the Java updates. Then, out of paranoia, I always run a full system scan.  My file counts always used to be, on a full scan, approximately 320,000 files.  Now, after the Java updates, I only get a file count of apprx 145,000.  What gives?  I assume that it is no prob bcuz Norton says OK to download each time (and Verisign is always confirming that the update IS from Java). Any worries? - Newbie Dave