H1B application I94 is different

Hi. I have my H1B petition in initial review status. The receipt date for the petition says 9th April 2012. After having applied for H1B, I had to go back to my home country (INDIA) for personal reasons and I find that I have a different I-94 record than what I had submitted at the time of applying for H1B. It never striked me about this change before leaving the US. Now I am worried if at all for this reason I will have a difficult time to get the outcome for my petition or if at all that can have me rejected for my H1B. If at all it does not make that difference to H1B application and lets say I am able to get an approval witiin few weeks, is there anything I need to do for having a different I-94 record to that applied for H1B with? I mean am I then required to go back to home country again and get it stamped and reenter the US with a new I-94 record?

If you filed your H1B petition w/ COS, USCIS will reject the COS application and consider only your H1B petition since you traveled out of US during petition process time. Now to move to H1B status on 1st October, you may either exit and re-enter US with stamped H1B VISA or apply for COS by September end.

Thanks for the reply Sujith. I am not clear when you say that I have to apply for COS by september end. I mean is it only required to apply for COS before september end for me to be able to get effective with H1 or I have to have an answer on COS before september. If I am not wrong it usually takes around 2-3 months for COS result and lets say I get my H1B petition answer by July end then even if I apply for COS by august first week, I cant be sure of me being able to get an answer on my COS application before september end. So then in such case what happens? One more thing can I make my wife apply for her H4 visa immidiately after my H1B approval? And in such case what happens to her if I dont have the COS answer by the time she goes for her H4 inerview. I still have valid OPT until next July…