I am having the same problem. Disk usage analyzer says:

Total filesystem capacity: 107.2 GB (used 84.8 GB, available 22.4 GB)

So far, so good. But, under "/" there is only 12 GB used, not 84.8 GB.
DUA does not tell me where/what the difference of 62.4 GB are.

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Disk Usage Analyzer does not detect files in the directory
https://bugs.launchpad.net/bugs/114341
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