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Hoi Alessio,

I think  the chi2/ndof calculation  for the tree-based  comparisons is
confusing (at  best), especially when comparing with  the numbers from
the histogram based comparisons. Looking e.g. at the lower plot of

  http://www.slac.stanford.edu/BFROOT/www/Physics/Analysis/AWG/InclusiveSL/islrecoil/datagene_ChB0909_80fb-1/comparison7nchgallcuts.ps

one  would conclude  from  the number  printed  on the  plot that  the
chi2/ndof is  quite ok. Looking  at the plot  it is obvious  that with
only one  point showing agreement within  one sigma and  all the other
FAR off, the  number cannot be correct.  

I would suggest that this improvement  should be the next task on your
to-do list (at least when working on this topic).

Cheers,
--U.