Hello,
I am an polish citizen and J1 researcher working at state university since May 2006.
I was entitled to a 2 years exemption form federal taxes. I applied for tax return for years 2006 and 2007 and received the full refund on them.

My plan was to come back to Poland early 2008.
But in November 2007 my son /he was born with some birth defect/ had a surgery in US hospital. After some time passed it occurred that the surgery must be redone.
The second surgery was conducted in November 2008.

Since I have been offered to stay at university longer and I haven't been sure if the proper treatment could be accessible to my son in Poland I've decided to extend my visa and stay in US longer.

I know that individuals from some /but not all/ countries will retroactively lose treaty exemption if their stay in the United States exceeds the time limit allowed by the treaty.

Now I'm concerned –I can’t find a straight answer to my question - I exceeded the two years stay in US in May 2008 and I extended my J-1 visa in 2008.
Did I lose the treaty exemption retroactively? Do I have to pay the taxes back ?

According to the official site of Kansas State University I didn’t.
Here is the link:
Non-Resident Alien Employment Tax Treaty Summary-Payroll & Employee Data -Division of Human Resources at K-State (http://www.k-state.edu/hr/ped/treatysum.htm)

Can anyone help me ?

There is NO retroactive tax provision in the Poland-U.S. Tax Treaty for researchers claiming the two-year tax exemption.

Hence, while your income DID become subject to U.S. income taxes the day after the 2nd year anniversary of your arrival, you will NOT have to pay two years worth of back taxes retroactively for 2006 and 2007.