Low RNA quantity after on column DNAse digestion - (Mar/04/2014 )

Dear All, 

I am faced something strange. I tried two time with different DNAse digestion which I am sure is RNAse free, to remove the genomic DNA from the RNA samples just prior to a deep sequencing experiment. 

Is there are any other reasons that the RNA is reduced in quantity after on column digestion ?

please suggestions to correct 

RNAse contamination from your pipette or water?