Hi Team, i have enabled withholding tax suite app, in an invoice of amount 100, 10% withholding tax is added, now if i receive customer payment of 90, invoice still shows open instead of fully paid. Am i missing any configuration here?

Do you have a VAT code with zero rate? (Typically undef). If not, then this may be the cause (you should have a tax code with zero rate as the WHT bundle will create a transaction/line with this VAT code, if the bundle can't find it, then it will fail to create anything)