That's an easy one. The drive capacity shows the real amount of data stored. When you highlight all the folders and check the space, it will only count the files that you have access to. Some folders (like System Volume Information) have no permissions set and they show as 0 bytes when you check its properties, even if there are some GBs worth of data inside.
Advanced info:
If you wanna take ownership of all files in a disk (Only recommended in a single-user environment) go to properties on your disk, security tab, advanced, owner tab, and take ownership of everything from there. It may cause some "Access denied" if you reinstall your system, as the new user won't be the same, even with the same name and password. But you can give ownership to a group, and administrators should be that group.
I have a 300 GB Seagate myself and I gave ownership of every file and folder to the Administrators group so I can access every file on the volume and reinstalls are not a problem.
Damn, I'm pretty sure I murdered some grammar up there, but this isn't my native language. Sorry in advance!