Sam:
You filed correctly! You had not yet met the Substnatial Presence Test, so filing Form 1040NR was correct.
Dual status was an option, but it was your choice, not a requirement.
Getting the improperly-withheld FICA (Social Security and Medicare) taxes back is a separate process from the annual tax return, and requires submission of Forms 843 and 8316 plus some support documents.
But FIRST, you need to petition the employers to refund the money, because it is faster and easier to get the refund from the employer than directly from the IRS. The IRS requires this.
Note that only the OPT period is exempt from FICA (Social Security and Medicare) taxes. You became liable for FICA (Social Security and Medicare) taxes on 1 October 2008, the date your H-1B visa became effective.
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