How can I diagnose and repair missing drive space?

I have a small ext3 / partition on a 2T drive which appears to have a discrepancy in its free space. How can I determine what is causing it and how it can be fixed.

After trying everything I could think of, I forced a fsck on boot which didn't have any affect.

I have other systems configured identically which don't exhibit this condition.

# df -h /Filesystem            Size  Used Avail Use% Mounted on/dev/sda1             9.7G  8.9G  318M  97% /# du -shx --max-depth 1 /5.2G    /# lsof | awk 'BEGIN {t=0} /(deleted)/ {t+=$7} END {print t}'0# tune4fs -l /dev/sda1 | grep -E 'state|Free|Reserve|size|Inode'Filesystem features:      has_journal ext_attr resize_inode dir_index filetype needs_recovery sparse_super large_fileFilesystem state:         cleanInode count:              2621440Reserved block count:     131029Free blocks:              212317Free inodes:              2487281Block size:               4096Fragment size:            4096Reserved GDT blocks:      639Inodes per group:         32768Inode blocks per group:   1024Reserved blocks uid:      0 (user root)Reserved blocks gid:      0 (group root)Inode size:               128

Edit:

fsck says the partition is 2% non-contiguous.

For comparison to du above (sparseness):

# du -hxs --apparent-size /4.9G    /