I set up my paycheck in Quicken using the paycheck wizard using the gross amount with deductions method. All of my payroll taxes, pre-tax deductions, and 401(k) contributions are set up in the reminder, and the Net Pay amount shows correctly in the "Track Paycheck" section.
However, in the Bill and Income Reminders widget on the Home screen, the amount field is always wrong when I open Quicken. Rather than showing a deposit as the net total of the income reminder, it actually shows my 401(k) contribution (Employee contribution + Employer match) as a negative value on the reminder. If I go to "Edit this and all future instances", change absolutely nothing, and hit "Done", then the reminders update to show the correct amount as an income for the deposit (my net pay) until I close Quicken. The next time I open Quicken, it reverts to the incorrect negative values.
I have tried validating and super-validating my data file and that doesn't fix the problem. I have also tried deleting and re-creating my paycheck reminder, and that also doesn't fix the problem.
I'm using Quicken for Windows R65.29. I've been having this problem for about 5-6 months, right about the same time as Quicken started to use the new bill pay system (I don't use bill pay at all).