Since the Integrity Checker monitors changes in some parts of the system (files, folders, boot sectors) it can more easily track down viruses the program isn't familiar with. The Integrity Checker displays warning if some of the information registered in the database has changed in any way. A change doesn't necessarily mean that the object in question is infected, however changes in certain files can be suspicious.
It is important to keep in mind that not all warnings F-Check reports because of changed objects are because of viruses or other security threats and with a poorly defined set of objects (files, directories or boot sectors) F-Check can generate many such warnings. In those cases F-Check should not be told to try to fix the object in question.
Special care should be taken when dealing with boot sectors or MBRs that have changed, although F-Check includes tools which will let the user undo any damage in most cases.
When a new operating system is installed or the hard drive is repartioned it is normal for these objects to change and asking F-Check to fix them might result in the system not rebooting normally.