Income tax refund

I had filed an online return of income having refund status for AY. 2009-10. The central processing centre , Income tax Deptt, Bangalore has intimated on 29 Dec 2011 that the refund was not processed by them and I should contact my jurisdiction officer. I had filed income tax return based on the jurisdiction based on my employer name. The jurisdiction based on my residential area is different.The income tax website shows my jurisdiction based on my PAN number (residential area). Where should i file an application for further processing of refund?

Will there be any applicability of time limit of 1 year as per section 237-239 of Income Tax Act.