I think its the way files are counted and how they're scanned. You can run 3 different AV's and they give different file counts.

Scan all files would be every line of code on the PC, that could be a lot if each is counted as a file scanned

For years my XP home OS has always had about 120,000 files.
What program was giving you this file count ? and how much has the file count changed with this program ?

And don't forget about System Restore and how it changes things