I've heard such a thing a few times before... but we were not able to reproduce this behavior (and have no idea why such a thing would happen).
Could you please give us as much detail as you can?
E.g., what type of scan was it (as DavidR asked) - archives on/off, sensitivity... was it scan of "local disks", or rather "folder selection" with C: and D: drive selected? Does anything change if you change the scan type, or select a different area (C: drive only, for example)?
You can turn on the creation of the report file and select everything (even "OK files") to be included there. The report will certainly be quite big, but it would be interesting to see if it really scanned the whole drive, or maybe restarted somewhere before the end...
What kind of partitions do you have? Any SUBST-ed drives, virtual folders... or so?