Intimation under Section 143 recd

Hi..

I need suggestions on this. I have recd an initimation under section 143 at my previous residence in chennai asking me to pay taxed for fin year 2008-2009. I am a salaried employee and my company has remitted TDS and in the form 16 they have mentioned all the details. Per form 16 i have no more tax liability since all taxes were paid upfront via TDS. The intimation, how ever has no mention of any of TDS and has directly taxed me on my taxable annual income , which is indeed a sad affair! :( Anyways following is my issue...

I could not file tax returns for fin year 2008-2009 since I moved to US since oct 2008. I still work for same company.  I wanted to know if this can be closed if i just file my tax returns now. .Also will there be any penalty for late filing, am not aware since i have never filed it late before. And any simple interest that I need to pay although all the taxes had been paid upfront?

Many thanks for your suggestions..

Thank you

Radhika