I am Indian and my company has both India and USA operations.
I came to USA on 01-July-2007

Initially due to project uncertainties I continued to be on payroll of Indian branch of my company from for 4 months July-October.
During this time the Indian company paid me My Salary in India (after deducting Indian taxes), Accommodation on sharing basis, car on sharing basis and an allowance $50 / day (per diem).
We took the per diem from the traveling advance which the company gave us.

On 01-Nov-2007 I was transferred to the US company which started paying me my salary (after deducting US taxes).
My Indian salary / per diem and other benefits ceased from 01-Nov-2007.

My W2 showed the salary for the Nov-Dec.
I checked for my status with the help of a tool on one of the websites and it said I am a resident alien.
I filed my return with form 1040EZ and got a refund for all the tax paid for the 2 months.

Now I am having doubts whether am I a resident alien.
And If not what should I do to get my returns corrected?
Will I have to pay tax again for the salary received in India?

Your help will be appreciated.
Thanks in advance.

It would be incorrect to file as a resident for all of 2007. You have a dual status situation and should file dual status. See the IRS website for details on how to do that.

Thank you