I moved this to the VirusScan community. Hopeflly someone can help you soon!
The logging/reporting aspects of the scanners has always been a challenging area.
I verily believe there are inconsistencies and issues to be identified and solved here, the problem is in identifying them. If you have a test case scenario that reproduces the mismatch you're referring to, please contact McAfee Support with the details.
However, you might check on what the log size limit is set to. We truncate data from the logs when the limit is reached.
Thanks for the information. I can tell you that it is not due to the log file getting truncated because I can see this issue appear several times within the same log file. For example, the log file starts off with a bunch of deletes of third party cookies, then I get the summary information that states a large number of files have been deleted. Then I get another list of deleted third party cookies which is then again followed by summary information that states a lot more files have been deleted than have been logged previously.
As for reproducing this issue, I have no idea why but it happens consistently on one machine. However, I certainly have no idea about what I could provide to mcfaee support.