I see the same thing. df -h shows 28g for / and baobab shows it is full at 3g
Baobab is not reading the partition size correctly. Directories underneath the 
partition show correctly but on my drive with a 28g / and 165g /home it shows 
the root of the drive incorrectly (shows the total used vs total available).

** Changed in: baobab (Ubuntu)
       Status: New => Confirmed

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baobab shows hard-disk usage wrong
https://bugs.launchpad.net/bugs/385339
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