As GrandFather has said, there are some native Perl ways of doing this, however, it may be just as easy to use the -f option with shutdown which forces any open applications to close.

This is a "safe" shutdown from the point of view of Windows, i.e. it will stop the OS cleanly so it shouldn't winge on the way back up. You will lose any unsaved data in applications though.

From your description of Windows checks for errors on starting again, it sounds as though you're using Windows 95/98/ME (but I could be wrong) - switch over to XP Pro and NTFS and you shouldn't have these problems :)