Most cytometers use the impedance method for cell count.
Any change in the electrolyte state and distribution of electric charges in the cell suspension medium may interfere with the count.
Such could be the case after separation in density gradient. I recommend the washing of saline cells and their resuspension in compatible plasma or better in a mixture plasma-red blood cells (separated by centrifugation).
Let me know.
Alternatively and without additional manipulation the "old" Burker method could be, although time-consuming, resolutive