A theoretical point that explains this type of result is that cells may be
arrested in S-phase before the addition of the BrdU. BrdU is only
incorporated into cells that are in the process of synthesizing DNA. Any
cells that have started to synthesize DNA before the addition of the pulse of
BrdU -- but then for some reason have quit and are arrested in S-phase --
will show up as S-phase cells in a PI staining procedure, but will not be
BrdU-positive.
This might account for your findings....