Thanks guys; I called Merrill Lynch, the stock option program admin.
They confirmed that they sent me a letter (1099B looking doc) for the transaction indicating the amount of federal tax withheld, but they did not do the actual witholding - even though the trade confirmation suggests they did. Apparently my employer witheld the taxes and reported it on my W2.
When I did my return, I added the ML tax witholding amt to the fed tax paid (over and above my W2) essentially double counting it. Since the IRS did not receive any tax witholding from ML, they claim I owe the tax amt on the transaction, plus interest, plus penalty of course.
This seems stange to me... why would ML do the transaction, but my employer withhold tax - it was not treated as W2/wages. I have no recourse to prove otherwise, as ML did not send any tax to the IRS.
What's worse ... I did the exact same thing for FY06, so I can expact to receive another letter soon.
Grrr...