OK, I have clarified this a bit further and I believe this to be the position.
Where the mortgage contract allows the lender to charge legal costs for chasing arrears, they can charge them, up to the period just before issuing court proceedings.
However, the costs of court proceedings are a matter for the court alone. They cannot charge you for issuing court proceedings if the Registrar or Judge has told them not to.
I understand that if the Registrar makes no comment on costs, but just strikes out the proceedings, then they can charge costs.
So, if you reach an agreement with your lender after proceedings have been reached and they tell you that they are going to apply for an order to strike out the proceedings, then you should go to court. Stand up when the case is called and ask the Registrar for an order that no costs are to be awarded. The practice in Dublin is to allow no costs, where no formal order is made.
If your lender has added costs to your mortgage without a court order, then you should challenge it.
As itsallwrong says, go to the Circuit Court Office and ask them do "draw" the court order in your case. The Registrar actually makes an order to strike the case out.
Send this to your lender and ask for a refund.
Brendan