If there is no shunt resistance (a short circuit) then you have contact between your electrodes. It is likely that your layer of silicon is non-uniform and may have gaps.

This could be caused by damage from the proton beam, or when you deposited your silicon film it may not have wetted the substrate very well. Perhaps you could do some SEM on your films before and after proton beam treatment.

Dust contamination can also cause short circuits, or at least significant shunting; dust particles can be microns in size, and if this is greater than or comparable to the thickness of your film it will cause a short circuit. If this is the case you should clean your substrates more thoroughly.

Please Srikanta can you display the IV characteristics of the solar cells before and after the proton implantation.  From the principle point of view, It is so that the proton bombardment causes damage of the crystalline structure in the penetrated layer converting it to amorphous structure. The amorphous silicon has a very high resistivity. To restore the crystalline structure the material must be annealed at relatively elevated temperature may be as high as 1000 degree centigrade. I can also annealed using a laser beam which causes local melting of the damaged layer and re crystallization on cooling. 

wish you success