Tried switching 'Allocated Space'. Changes by quite tiny numbers...
nowhere close difference I'm having.

btw also tried on ext3... does the same thing.
As I said it apparently this happens with folders with large number of files in 
several levels of sub-folders. (At least it is easily noticeable for these)

also forgot to mention I'm using x86-64 system. (I don't believe it
changes anything, though)

I might later try various LiveCDs with baobab (both x86 and x86-64).
I might also try upstream version of baobab.
However this bug report is still relevant to this particular version. (being 
Baobab 2.24.1 in this case)

** Description changed:

  Binary package hint: gnome-utils
  
  I've noticed the baobab (aka Disk Usage Analyzer) is not reporting sizes of 
directories correctly.
  I my particular case all scanned subfolders are readable (and even writable) 
for user, so that is not a problem.
  
  From what I can tell, it calculates the size by scanning it's largest 
sub-folders and summing them up.
  This however leads to errors, when there exist large number of smaller 
directories of files one or more levels down. The calculations apparently 
discard these as unimportant, yet those numbers add up and may make quite a 
difference.
  
  I've attached a screenshot to this bug.
  Focus your attention on "misc" size in baobab vs. nautilus.
  And also "windisk" size against Volume size in misc's properties. (there is 
only 5 GiB free)
  
  I think the size calculation must be adjusted (even if that would mean longer 
scanning times).
  Accuracy is more important than speed.
+ 
+ Affected platform:
+ Ubuntu 8.10 (Interpid) with Linux 2.6.27-11 generic amd64
+ Baobab 2.24.1 from gnome-utils package 2.24.1-0ubuntu1

** Tags added: baobab

-- 
Baobab reports incorrect sizes
https://bugs.launchpad.net/bugs/341141
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