Bingo! That was going to be my next question - what were the tax attributes of the 401k account?
Tinkering around - I have been able to duplicate what you were seeing in the Tax Schedule Report.
I do not agree with the QW rep who recommended setting the 'Transfers In:' attribute for a QW 401k account. That was the source of your problem.
Bottom line - when using the Paycheck Wizard in combination with a QW defined 401k account, leave the 'Transfers In:' tax attribute blank for the 401k. QW handles everything correctly without setting this attribute. Setting the tax attribute for the 401k confuses QW and results in errors in QW's tax reporting.
The recommended tax attribute for 'Transfers Out:' is correct. I have mine set that way and am making transfers out and QW reports the transfers out correctly as taxable income. These transfers out are indeed reported in a year-end Form 1099.
Did this clear up your original problem with the Tax Planner?