I have been on F1 visa since Aug 2003. In Oct 2008 I got my H1, so as I understand, 2008 I should file as a Resident Alien since it's more than 5 calender years. Assuming that is correct, my question is, that till I got my H1 in Oct 2008, I was working on the F1 visa from Jan'08 - Oct'08. For that period no S.S. and Medicare taxes were deducted(since it was F1). However if I file as a resident for 2008, does that mean I owe the S.S. and MEdicare taxes from Jan to Oct of 2008?

Thank you for your time.

Yes, you were required to pay FICA taxes on your F1/OPT income during 2008.
IRS may contact your employer and then you employer may contact you. If they do contact you, you must pay it back.