AFAIK VAT on rented residential property is no longer claimable since early 2007. ( before March 2007 anyway) This was removed in Finance Act 2007. Furthermore even up to then registration for VAT for such type of enterprise was by election to register not by requirement to register. Normally one can not back-date an elected registration so this may be Revenues reasoning on your claim even though they did issue VAT returns back-datd. You can ask your accountant to appeal to Revenue but not sure if you would succeed.
Incidentally, regardless of the back claim, while registered you are obliged to remit VAT on the rent. You might need to discuss with your accountant the advisability of continuing this course if the initial claim proves unsuccessful.