well...what do you scan (MAME, iso images ;)) and what's your turned on options? E.g. if you scan with sha1 checks enabled on huge files, it may take a while.....
Also again, try to disable a possible virusscanner (at least for the rompaths).

You can't compare a scan (which does some random access/seek operations to the file) with an OS' copy operation


Roman Scherzer