I'm looking at a scan log for one of my computers.  One column is for "Omitted".  Are these files omitted because they've been scanned during the day by File-System Auto Protect?  I ask because on this particular computer I've temporarily turned off Auto Protect to troubleshoot performance issues.  With auto protect on the omitted files are over a thousand.  With it off there are only a handful of files omitted but the total number of files scanned doesn't change that much.