Hi,
I had a similar situation few years back.
This is what I did at that time,
I spoke to our HR dept and they confirmed that they always make deduction based on the instructions given by Revenue.
After getting that confirmation, I wrote a letter to revenue and said that the mistake wasn't made by me so revenue has to take the responsibility for giving wrong instructions to our HR dept & also attached our HR dept confirmation mail.
Also I informed revenue that I could pay the under payment by instalments. Revenue agreed for this arrangement and they deducted my underpayment tax from my tax credits in the following years.
regds
Joel