Reversal of former IRS late payment penalty upon amendment?

If I amend my 2009 tax return to reflect additional, missed deductions, such that my taxable income is reduced, will this also serve to reduce or eliminate the late payment penalties (not enough money withheld during the year - i.e., paid all tax due by 4/15/10, but the IRS wanted more withheld, earlier in the year), or are those non-waivable once essed, regardless of any later amendment to the return? Thank you.