You need to define a tolerance group for customer in config.
Normally you can do this by Company code.
the standard tolerance group is blank.
In this you need to specifiy how the customers who have that value in the customer master can clear, i.e. amount and %age.
If you have defined a tolerance group it could just be that you need to assign it to your customer(s).
If you want to apply it to all customers look at doing this via t code MASS.
Hope it helps.