Are you integrating the valence charge? I'm going to cut-and-paste from: http://theory.cm.utexas.edu/bader/vasp.php
Note that the partitioning is done on the total charge (CHGCAR_sum) but the integration is done on the normal CHGCAR file from vasp, containing only the valence electrons.
By adding the LAECHG=.TRUE. to the INCAR file, the core charge is written to AECCAR0 and the valance charge to AECCAR2. These two charge density files can be summed using the chgsum.pl script:
chgsum.pl AECCAR0 AECCAR2
The total charge will be written to CHGCAR_sum.
The bader analysis can then be done on this total charge density file:
bader CHGCAR -ref CHGCAR_sum