anything thats wrong will show up on the screen during the scan.
If you want to see,
Right click on my computer => manage
Select Event Viewer then applications
Look for the latest Winlogon(should be just after you ran chkdsk) under source. and the log should be in there.
Don't forget that the Recycle Bin and Restore Points also consume space which isn't shown in a lot of space analysis programs. You can click on the Recycle Bin to see what it contains, but getting information about Restore Points can be a little more difficult. This article contains some useful information about them: