If you are checking the free space by selecting the folders, you are doing it the wrong way.
The correct way is to right click the drive and select Properties. *The Pie graph is correct. *
Even more correct is going to Computer Management under Admin Tools and selecting Disk Management.
I'm pretty sure there is an obligatory Old New Thing blogpost about this.
The long technical explanation has to do with security. When you select all folders and use Explorer to calculate the space, Explorer is adding up all the files and giving you size.
- But what if Explorer can't see certain files?
Windows hides certain files from Explorer for a couple of reasons. One is for organization and a streamlined user experience. The second is to keep users from breaking their own systems. If you go under Tools/Options, there should be a check box for hidden files and protected operating system files. If those are checked, then selecting all folders obviously isn't going to select all files that exist.
Other caveats include Explorer does not add the size of alternate data streams, ever.
The pie graph, 99% of the time, is correct. The only big factor you worry about is that the pie graph is constrained by your user quota, if it exists. Selecting files and right clicking for the size was never meant to be a definitive answer. Not so much a case of Explorer was lazy, but it isn't the right tool for that job.
I hope that helps.