My company did not deduct SS and medi care from my payroll as I started H1-B last year Oct. they probably did not update my visa status in the system. I will have the due amount paid this year.

My question: will this affect my 06 tax return?

Since SS are after tax deductions, it seems to me that filing my tax return with the SS fixed later is OK, right? :)

OK, my answer found out: no.

You are right, the answer is no!