Dear Surendra,
please clarify whether u have posted the invoice for the vendor.in such case i think you have to provide a base amount in FB60 for W/H tax deduction tab(that is deduct the down payment value for which already tax deducted from the invoice amount so that while posting FB60 W/h tax amount is calculated only for the balance amount and in eventually while processing F-53 u will not have issues related to W/H tax.Hope this helped.
Thanks
Nagendra Prasad BS