Income tax question

Hi,
I'm a resident of Northern Ireland working in the Republic of Ireland.
I pay income tax and PRSI in the Republic of Ireland (ROI). However, as I'm a resident of Northern Ireland, I obliged to complete a tax self assessment each year to HRMC.
In previous years, self assessment calculated that I owed some tax to HMRC (income tax paid in ROI was less than what was due to HMRC). I was due to pay the difference to HMRC, which I did.
However, in recent years, since the income tax levels in ROI have risen, self assessment has calculated that I have overpaid income tax. I understand that the Double Taxation agreement between ROI and the UK means that any tax shortfall should be paid. Overpayments would not be refunded though. However, for the past few years, after completing self assessment, HMRC have refunded me overpaid tax (£2000 for 2012/13 tax year). I'm pretty sure I've completed the self assessment form correctly- entering income and tax paid in the foreign income section. I'm unsure as to why HMRC would be repaying me income tax that has been paid in another country.
The only reason I can think of is that I work for an Irish company that's parent company is in the UK. Would the fact that the company's head office is UK based have any bearing on this.
I'm reluctant to contact HMRC directly as I don't want to find out that they've made payments in error and want all over-payments returned?

Thanks