Why am I being charged a penalty when taxes paid through withholding or estimated payments were always higher than owed?

The U.S. tax system operates as a pay-as-you-go system. What this means is that you must pay your taxes as they occur.  For example, If your estimated tax payment for any quarter is less than the amount required for the income earned you will incur an underpayment penalty.  This penality is not deleted by any future estimated tax payments even when the estimates exceed the minimum required to avoid a penalty for the quarter.

under normal 2210 rules even though the w-2 was in the first quarter the withholding is spread out over 4 quarters.  the way around this is to check box D on the 2210 and then enter your actual withholding for each quarter.