Well the cynical answer is simple economics. In the original tender there were multiple bidders competing for the contract. I would assume that if there was any option for extra units in the original contract, it's long expired. Bottom line is there is only one supplier (and certainly only one supplier who can produce them reasonably quickly), and IÉ have to pay what they want to charge.
A slightly less cynical answer is that Hyundai/Rotem have to dust off a 12-year old design for a relatively small production run, so it's only natural that costs have risen.