Thanks Jes and Pippin.
Well, the thing is - I work for Canadian Company, and that is clearly mentioned in my reference letter, and evident from WP, pay slips, T4, assessment record etc. All of these I have provided to CIC. The only gap was the letter was written in US letterhead showing US address.
My HR has clarified in a separate letter that as per our company policy all reference/verification maintained by corporate HR. Incidentally they are located in US division!
Thanks again.