Hi krishnad,
I had faced the same problems.
There seems to be a bug when the BSSE is calculated with DFT-D3 methods.
The error is appearing in the 'ghost' calculations with the DFT-D3.
One way to avoid it, is to calculate the BSSE without the $disp3 keyword , and then add the counterpoise correction to your total DFT-D3 energy of the dimer.
You should also include the deformation energy of the monomers into the formula of your binding energy. So, your final binding energy should include 7 terms, as is calculated from the jobbsse script. Check turbomole manual and also these notes useful notes:
http://vergil.chemistry.gatech.edu/notes/cp.pdfHope that you can solve your problem.
Regards,
Andreas