I, too, found that my return was rejected when I had Box 11 Non-qualified pension (I don't remember the exact wording). In my case, the W2 was for imputed income for life insurance plus the non-qualified pension plan. You are correct... the boxes below 1 & 2 add up to the box 1 & 2 numbers. The cause appears to arise from the question that you are asked after entering the W2 with a box 11 amount in it. If you answer, "yes, this was a withdrawal of cash", it'll trigger leaving the box 11 amount from your 1040 wage line and add the box 11 to the schedule 1 (other income) line on the specific line for "non-qualfied pension". This will be added to your income on page 1 of the 1040 under "other income". Hence, you're taxed on everything but the box 11 under wages and the box 11 on other income. On the other hand, if, after entering the W2 info into Turbo Tax, you click on the box "No, this was contributed..." (I don't remember the wording), all of the taxable income (including line 11 non-qualified pension) shows up under wages. Hence, you're paying tax on line 11 either way at the same rate. One could argue that the first is probably "more correct", however, the end result is that you're paying the appropriate tax on the income from wherever. When you check the no box, the electronic filing works.
Just to clarify, go back to your federal input...go to inputting W2, click the edit (if you don't do this, you won't see the yes/no box to check). Verify the info on the 2 screens, save the W2, it'll say "you're refund is Xxx" and then the next screen will have a question (I don't remember) and then the next screen is the question about the non-qualified income.
Good luck.
