Income Tax return - Different Experience

I changed job in December 2008 and moved to Pune. I joined small company called Maniks Systems.
Till December 2008, Total Rs. 826 was deducted in Avenues as Tax at source. At Maniks, there was no deduction of Income tax as per Salary from Mid December to March 2009. But if total salary income at Avenues is also considered then i was eligible to pay more tax. I was not aware of all these income tax stuff that time.
Next year, I joined Tieto and submitted Form 16 by Maniks as per request by Tieto. My tax deduction was done properly by Tieto considering Salary of Maniks as well during Financial year 2009-10.
Now I realized that during last year(2008-09), Tax deduction was not correct and i should pay some tax. I searched on net regarding the same and came to know that I can pay self assessment tax.
I didn't have salary slips of Maniks (for month of December2008-March 2009) as I got last 3 months Salary slip at the time of relieving in January 2010.
I decided to do simple calculation (even though i was going to pay more tax). My salary at Maniks was 30000 per month. I joined in mid December.
Details of Salary received (Only deduction was professional tax)
Dec 08 : 13800/-
Jan 09 : 29800/-
Feb 09 : 29800/-
Mar 09 : 29800/-
Total Income = Rs. 103200/-

I was having Form 16 from Avenues for year 08-09 and Income chargable under head Salaries was Rs. 176081/-
Deduction done at Avenues: 34191/- (LIC premiums till December)

I calculated Total Income as Income in Maniks + Income as head salaries in Avenues
103200+176081 = 279281/-
Here I was at loss as I have not considered any deductions for salary at Maniks (like Travel allowance, medical, HRA).
My total LIC premium for year was 37014/-
I was also paying for my education loan and got interest details from bank which was = 2034/-
So I filled ITR as

I paid Rs. 11133/- as self assessment tax using Axis bank online tax payment faciltiy and Filed Income tax return and posted to Bangalore office.

I received Income tax intimation notice by post under section U/S 143(1) In September 2010 for the same.
By Mistake, Income tax office did not considered Self assessment tax paid by me and asked me to pay Rs. 11301/- (with interest).
I paid my tax properly still i received tax intimation so i was very confused. I mailed them details of my tax payment but did not got any reply. I contacted Bangalore office and they told me to send my reply by post if i have already paid the amount with necessary documents as proof.
I searched on net for details how to reply to tax intimation letter. I sent them my reply with Subject as "Rectification as per section 154" by post with necessary documents. (self assessment tax paid receipt, form16 of Avenues, Tax intimation letter, ITR details).

After few months, my ITR status was updated as No demand/No Refund on income tax website.