Payment Discount Tolerance Dates not working in Dynamics NAV?

I'm trying to setup a NAV 2009 R2 to use the Payment Discount Tolerance Dates, but no matter what I try then I cannot get it to work.

What I've done:

1) Setup of the "Payment Discount Grace Period" in General Ledger Setup to 14D

2) In cash receipt journal select a customer using Payment Discount and the amount received (invoice amount minus payment discount).

3) Select apply customer entries.

Now I can see the invoice and the remaining amount, remaining payment discount and the payment discount tolerance date. But when I select to Apply the payment to the invoice, no payment discount is taken.

I have tried this both in Cronus NAV 2009 R2 and NAV 2013, same problem.