Very weird, I can think of some things I might check:

• It is possible that you have files on disk that don't have a filename anymore. This can happen when a file gets deleted while it is still opened by some process. Only the filename is gone then, but the file still exist until that process gets killed. If this were the problem, it would go away if you rebooted, since that kills all processes.

• Maybe it is file system corruption. Try running fsck.

• Maybe the files are impossible to see for baobab. Like if you had gigs of stuff under (say) /home on you root fs, then mount another partition as /home over that, those files would be hidden behind the mount point. Try booting into a live usb and checking your disk usage from there, when nothing is mounted except root.

• If you have lots and lots of tiny files, that can in theory use up a lot more disk space than the combined size of the files would, because on a lot file systems, small files always use up some minimum amount of space, and each file also has some metadata. This would show up as some discrepancy between du and df output. For me, df --inodes / shows ~300000 used, or about 10% of total. Each file, directory, symlink etc. should require one inode, I think.

• I have never heard of baobab, maybe that program is buggy or has some caveats. Does du -shx / give the same results?