Notice under section 139(9)

Vicky (Others) (41 Points)

24 October 2014  
I've recently received a notification 139(9)to pay IT amount even after paying it.
Below is what I've done in July2014:
1) I've filed my IT Returns with "tax payable" option and in the Final ITR there was some tax amount which I had to pay. I clicked submit and my form got submitted without asking me to pay the money for balance tax.
2) After that, I've paid that balance amount and filed a revised return under 139(5) immediately with "Nil Tax" option.
3) I've sent both the forms original and revised together to IT dept in Bangalore.
 
Now, I've received a notification under Notice under section 139(9) of Income Tax Act,1961 for the ORIGINAL (First) IT filing to pay the money in 15 days and upload the updated X M L.
 
When I tried to update the X M L using the utility, it is autocalculating some more amount to be paid by calculating it for the period from post filing date(July 2014) to till date(Oct 2014).
How can  avoid this and still update IT dept?
Also, I'm asked to provide Notice Date and Notice No? There are no such fields in the notice 139(9).
 
What Shall I do?
I'm worried about this as I paid the amount and they didn't even consider my revised return form sent together?