Hi Maggioneato,
Have you tried running Scandisk and Defrag in safe mode? It's a lot quicker and negates having to go through msconfig, as you only have system essentials running at startup in safe mode. For info on how to start in safe mode, see
here .
This is a problem that needs to be fixed, because it is meant to work, but in the future,I'd definitely recommend getting
Diskeeper Lite. The free version is fine, you just have to start the run on each partition one ata time. It takes a fraction of the time to run, but you still get the pretty screen with all the clusters being checked..

I'm a geek, what else would you expect..
Cheers
Liam