Linux different size for df and du for root partition
See if you have any deleted files still in use
lsof | grep deleted
There's a lengthy explanation to be found in any number of blogposts online with a quick search, but the basic gist is this:
If I create a 1 GB sparse file, du will show 1 GB, but df will show zero usage. If I have a 1 GB file open in some program and delete it, df will still show 1 GB of usage until all references to the inode are closed, but du will never find the file to display it.