I understand this as both the return are exactly same & are filed for the A.Y. 2007-08 only.
I understand that the would have been filed before 31.03.2009 as this was the last date even for the revised of the belated return for the A.Y. 2007-08.
I think u should file a letter with the income tax department i .e. with your Assessing officer stating therein all facts & mention dates on which returns were filed along with acknowledgement no. & also the Pan no.
I this is what u need to do. second thing that u can not treat the second return of the A.Y. 2007-08 as filed for the A.Y. 2008-09 as u have already comminicated that opening balances were of A.Y. 2006-07 only.(how there can be 2 Returns with same opening balances)
For any further query u can contact me on sunil.kotak @ money-matters.in
Sunil