I am having a similar issue with 9.04 AMD64 and Disk Usage Analyser.

When I do a 'Scan Filesystem' from Disk Usage Analyser it shows "Total
filesystem capacity:"... which are accurate and match df -h, but the
folder breakdown is vastly different from the above - Whilst the real
disk usage is over 320Gb, the total in the 'breakdown' list shows a
total of 37Gb.


** Attachment added: "Disk Usage Analyser"
   http://launchpadlibrarian.net/28241812/DiskUsageAnalyser.png

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df -a contradicts Disk Usage Analyzer. 
https://bugs.launchpad.net/bugs/370487
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