IT returns and EC

So, ok, I'm ready to take the plunge and post my documents to HO under the HSMP program. I must say that this is one of the most informative sites I've ever seen - not to mention the proactive participation of members. One final query - this regarding the EC in India, not the approval stage - and I'll be more confident.

I relocated, in Aug 2003, from the USA to work for the same company's subsidiary in India. I have the proper experience letter, from the US company (1998-2003), and the appointment letter from the subsidiary (2003). Though I've been working with the subsidiary in India since Aug 2003, I was paid in the USA for the fiscal years 2003, and 2004, and subsequently in India in 2005-2006. Will the IT returns that I will be submitting when applying for the EC in Chennai, India raise any eyebrows given the fact that though I was working with the subsidiary in India since 2003 my IT returns for the years 2003, and 2004 (W2) originate from the USA?

Moderators / Members, any inputs, please?