Conflict of manual v/s e-filling of return

I submitted a manual return for AY 2010-11 before July 2011, before the assessment was made I revised my return electronically in time.  The same was not entertained by CPC as they could not find the Original return in their records, hence sent back the same to my ward at Ghaziabad.  In the meantime Ghaziabad office made my refund as per manual return.  When I approached Ghaziabad office to enquire about my revised return wherein more refund was to be made, they informed that as their computer is not accepting the revised return electronically, they are undable to process my case.  I asked them why the assessee should suffer without any fault of his own and due to failure of Computer Software.  I went there more than 8 times and at the end before 31st March 2012 they asked me to file manual revision and withdraw the electronic return, which I did on 29.03.2012.  When I approached them recently on 06.06.2012, they showed again their inability to process saying that they are still unable to resolve the issue of Manual v/s Electronically filed returns.  I want to know that whether the deptt. can deny my dues only on account of failure of their system?  I am harassed a lot.